The Polish, Baltic, Finns and Ukrainians would drain many resources, and undermine its strenght if not satisfied to certain extent. Russia had to station more soldiers in 1905 Poland out of fear of full grown uprising then it sent to war with Japan.
It could continue as heavy handed centralist state, but it would make it unsuccessful.
The reason Russia had more troops in Poland is that it was fighting a war at the end of a single unfinished railway link against a power it underestimated and so most of its army, stationed on its western border as made sense, wasn't moved. If the Poles were such a threat to Russia, what happened in 1914?
During the First World War, all these groups inside Russia totally failed to make nuisances of themselves.
The Congress Poles were dominated politically by Dmowski's pro-Russian National Democrats. Militariy nsurrection had been discredited in 1863. Young leftist radicals willing to consider it had been driven into the wilderness in 1905 and the really determined ones like Pilsudski had ended up in Austrian paramilitaries, and of course during WW1 the Central Powers totally failed to blow up Poland.
All the large cities of Ukraine (even in Volhynia) had Russophone majorities in 1914 (or Yiddophone ones, with Russian as the language of government and communication between communities), and the Ukrainians served in the Tsarist army like everyone else. The core constituency of Ukrainian nationalists were the educated middle classes who organised the Tsentralna Rada, and the Directorate's army was a mash of student volunteers, German PoW units, and totally unreliable conscripts (these warbands mostly went Bolshevik or bandit as soon as Kiev fell). The workers and peasants weren't any more problematic than any other workers and peasants, nor the aristocrats and officers any less reliable (the Hetmanate was a piece of extreme pragmaticism by Skoropadskiy and his breed, and they showed their true colours as soon as they lost their German sponsor by turning Denikinite). And to cap it all, in 1917, while willing to accomodate the Rada and Ukrainian nationalism, Kerenskiy still denied that "New Russia" was part of Ukraine at all. Whether it was was pretty questionable.
The Lithuanian language was tolerated even before 1905 and again, where was the Lithuanian uprising during the First World War? To say nothing of Vilnius being a Jewish-Polish-Russian city with a German population rivalling its Lithuanian one.
The Estonian and Latvian national movements had benefitted from "Russification", which in their countries had meant bringing the totally Germanised education and administrative structures in line with Russian norms: it's a lot easier to learn Russian than to prove descent from a crusader knight. During WW1, Latvian nationalist volunteer units fought
for Russia after the Germans made utter pricks of themselves in Courland.
And the Finns, after Russification was given up as a dead letter, had been pretty content with their autonomy: conspiracies during the wars came to nothing much while Mannerheim was busy being a distinguished officer of the Russian army.
This may seem a somewhat utopian portrayal of Tsarist rule. Be assured, that isn't the case. Tsarist rule was a litany of woe for Central Asia and the North Caucasus. But it was you who raised those nations which were actually broadly content to work within the Tsarist system and never posed a physical threat to it, and of course Russian rule in all sorts of places has been revised into a bloodthirsty reign of terror rather than properly analysed.
While of course autonomy for all these place and inter-national harmony would be
good, I see no particular reason why any of the countries you named was a drain on Russian resources sufficent to drag down the state.