but there is evidence of churches and communities throughout the Maghreb.
Sadly my french isn't great, but if yours is any better -
http://rhr.revues.org/5401
I think you may be mislead there : this article is about
native Christian communauties, which existence let little doubt and that vanished by the XIIIth century.
It should noted that the article points the really delinquescent state of North African Christiendom.
In 1076, Gregory VII regrets that there is no longer in Africa the three bishops necessary to ordinate a new one : there's only one in Carthage and one in Bougia, recently named on the request of hammadid ruler al-Nasir for its new capital
It less disappeared trough persecution (the article point again that the alleged Almohad persecution is dubious) than the usual acculturation you can find as well in Egypt or Syria, without great clanic feature to support a small remaining communauty in the coast or immediate hinterland.
It says nothing about pilgrimages, and only mention by passing a relation with papacy (which should have been close to the reduced relationship that it existed with Mozarabs in Al-Andalus) as broader relationship with Latin Christiendom.
This would likely speed up the conquest aspect of the reconquista, even if the colonisation part doesn't speed up - IMO certainly one of the reasons it was very slow going, besides the lack of sheer military might.
Which would be wrong : Reconquista wasn't accompanied with a settlement effort (I choose to understand colonisation as settlement there), but this one was subsequent, without too much trouble (would it be only the presence of Neo-Mozarabs in the Xth from Christian States faciliting it).
Note that the process wasn't slow, but long which is not the same thing. Basically, between the early XIth century and the mid XIIIth century, almost all Al-Andalus was conquered safe Nasrid holdings (which were basically sattelized by Castille even then).
The problem was essentially
1) Military and being tied up with the desintegration of unitary structures in Al-Andalus and their reconstruction by Berber dynasties
2) Stability in Christian States : Grenada basically survived so long because Castille infighting and succession crisis.
In addition, the Northern Crusades certainly didn't use Merchant republics, and succeeded (over time)
The comparison isn't really fitting. As far as I know, Northern Crusaders didn't have to cross a large body of water to advance, their cores being closer and ways almost entierly terrestrial.
For what mattered Levantine and North African Crusades, Mediterranean Sea wasn't going to vanish : the support from Italian maritime republic for supply and transport is mandatory, or, at the very best, a strong royal maritime policy as Louis IX's (which carry some other issues to the creation of Crusader States in Africa such as not fitting the royal plans).
But if the Iberian Kingdoms IOTL were happy to attempted to conquer in N.Africa without Italian assistance, then I don't see why Iberian Crusaders, and Iberian Kingdoms wouldn't sponsor the same ATL.
Which wouldn't be a Crusade per se, but a continuation of the Reconquista effort. Incidentally, it was generally tought that the Reconquista had to continue on the other side of Gibraltar's sraight but that went butterflied away by the discovery of Americas.
A Castille/Aragonese/Portuguese takeover of Morroco, for instance, isn't too much improbable because it partially happened (Portuguese hegemony on Maghrib's coast, Spanish outposts on Mediterranean southern coast).
Which is far more debatable would be the characterisation of Crusade (would it be only because it would be tied to a proto-modern state, and not a whole social class) and possibility to go deeper than coastal control (the aforementioned exemple never went really this way, in spite of IOTL efforts).