Well, I dunno, but I personally believe that Finland is a good example on how a "Congress Lithuania" without Poland in the Russian Empire would develop. After all, in Russian Finland, Swedish speakers made up a majority in parts of the country, too (Turku region), and they used to make up as much as 15% of the population - and yet, Finland didn't end up Swedish-speaking.
The presence of the Belarusians does throw an additional variable to the mix, though.
There's also one more thing to consider - since Poland is, in this scenario, an integral part of an enemy nation, Russia might actually endorse the Lithuanian National Revival, as a way to eliminate the power of the potentially traitorous Polish-Lithuanian nobility (which, as you said, could still hold ambitions of restoring the PLC). Something similar happened in Finland in OTL to eliminate Swedish influence, and while the Russians suppressed the National Revival in OTL as a result of the 1863 rebellion, they notably reacted to it less harshly than to fighting against the Polish-Lithuanian gentry.