Contemporaries are a relative thing: Tolerant compared to the Latin west? Probably yes, but not as much as the early Caliphates.
Only the Umayyad Caliphate really, when they tolerated pagan Berbers and Jewish Arabs for a brief period. Other than that, the Byzantines were more tolerant than most of their Christian and Muslim contemporaries. In fact, the Byzantines viewed the Arabs and Persians very fondly for a long time especially in this earlier period.
An excerpt of a letter from the Patriarch Nikolas Mystikos to the Caliph of Baghdad in 855/866:
Two Sovereignties, That of Arabs and of Byzantines, surpass all sovereignties in the world, like the two shining lights in the firmament. For this one reason, if no other, they should be partners and brethren. We ought not, because we are separated in the ways of our lives, our customs and our worship, to be altogether divided nor should we deprive ourselves from communication with one another in default of meeting each other in person. That is the way we ought to think and act, even if no necessity of our affairs compelled us to it.
In 987/988, Basil II signed a truce with the Fatimids where the Fatimids were recognized as the protectors of Christians under their rule, and the Byzantines recognized as protectors of Muslims under their rule.
A mid-12th century poem by John Tztetzes shows that the Byzantines had a favorable attitude towards Muslims and Catholics at the time. (Although unfortunately anti-Semitic towards Jews). Quoted from
this post which references it from
Byzantium: The Surprising Life of a Medieval Empire.
One finds me Scythian among Scythians, Latin among Latins,
And among any other tribe a member of that folk.
When I embrace a Scythian I accost him in such a way:
"Good day, my lady, good day, my lord:
Salamalek alti, salamalek altugep."
And also to Persians I speak in Persian:
"Good day, my brother, how are you? Where are you from, my friend?
Asan khais kuruparza khaneazar kharandasi?"
To a Latin I speak in the Latin language:
"Welcome, my lord, welcome, my brother:
Bene venesti, domine, bene venesti, frater.
Where are you from, from which theme [province] do you come?
Unde es et de quale provincia venesti?
How have you come, brother, to this city?
Quomodo, frater, venesti in istan civitatem?
On foot, on horse, by sea? Do you wish to stay?
Pezos, caballarius, per mare? Vis morare?"
To Alans I say in their tongue:
"Good day, my lord, my archontissa, where are you from?
Tapankhas mesfili khsina korthi kanda," and so on.
If an Alan lady has a priest as a lover, she will hear such words:
"Aren't you ashamed, my lady, to have a love affair with the priest?
To farnetz kintzi mesfili kaitz fua saunge."
Arabs, since they are Arabs, I address in Arabic:
"Where do you dwell, where are you from, my lady? My lord, good day to you.
Alentamor menende siti mule sepakha."
And also I welcome the Rus according to their habits:
"Be healthy, brother, sister, good day to you.
Sdra, brate, sestritza," and I say "dobra deni."
To Jews I say in a proper manner in Hebrew:
[Anti Semitic bile that I have omitted due to its irrelevance and because its nonsense]
So I talk with all of them in a proper and befitting way;
I know the skill of the best management."
There was also a mosque in Constantinople, built for the Arab prisoners of war during the Arab-Byzantine wars, and many of the frontier conflicts ended in friendly exchanges and freed prisoners between the Byzantines and Arabs.
That being said, they are at war right now, and are not really showing much eleison if the populace is not willing to beg it from Kyrie every Sunday. Policy mostly set by frontier commanders who have not broken out of their raiding attitude and are not really ready to rule (Phokas opposed Tzimiskes going that extreme for instance, knowing that policy suited for raid is not good for annexation). Not the wisest thing to do long term of course, but they have a siege mentality in mind, and would need rather strong leadership to keep them in check. Leadership unfortunately is more willing to milk it for personal gain than consider long term benefits. Tzimiskes will be singing a different tune once the full weight of the crown hits him, but others might step into his earlier role. There is also a question of how much attitudes will change as this approach generates success.
Well of course, the Byzantines were both Roman and medieval, so they were very brutal on the battlefield against their foes, as their foes were to them. But that doesn't translate into being oppressive at peace (except against Christian heresies). Just look at Basil II the Bulgar-Slayer, who was unusually cruel to the Bulgar army commanded by Khan Samuel, but after the war, tolerated the Bulgarians, giving Bulgarian leaders court and administrative titles and allowing them to join the Byzantine elite. The people of Bulgaria, having no monetary economy, were allowed to pay taxes in kind rather than in coinage, an arrangement that kept the Bulgarians satisfied with Byzantine rule until additional taxes were levied in the late 12th century.
With the Fatimids, Kalbids, and Abbasids, there is no such bad blood but even that did develop, precedent shows that the war itself would be brutal, but the Byzantines would assume a pragmatic policy of integration after the conquest and see the elites of their enemies as equals.
For the Byzantines to try and violently suppress Islam in particular, instead of having a slow policy of peaceful conversion or indirect influence, seems out of character theologically and politically, as well as suicidal for any large empire which would face unrest and revolts.
The only way I could see them going down that path is if the POD was later, after the core of the empire in Greece and Anatolia has gone through more hardship at the hands of the Seljuks, and the Crusaders have also caused chaos and tension. Through extreme brutality one emperor is able to restore the hegemony of a collapsing, nearly destroyed Byzantine Empire which has already faced atrocities from Crusaders and Seljuks. Then the Byzantines might have a more Spain/Reconquista/Expulsion of the Moriscos type worldview.
Also, population transfers is a thing the Empire was known to do quite often for pacification: which I think falls under ethnic cleansing (and is what they are doing now, sort of instead of massacres). Not necessarily sending them to be gassed at concentration camps, but prime ships are not going to be used for the transfers or best physicians be made available.
The Byzantine Empire performed population transfers, but it was generally to strengthen lowly populated regions with extra settlers and soldiers, rather than to remove people, unlike various 19th-century and 20th-century atrocities.