I think it depends on whether or not you think the consolidation of Europe into nation-states that was beginning to take place right around this time could be butterflied away. Personally, I think the Pan-Ruthenianism that laid the groundwork for many of the old Russian states to consolidate into the Russian Empire might have even been present during the reign of Andrew I of Moscovy. He was subjecting a number of local duchies directly under the rule of Moscow before the Tatar invasion in 1477, though with mixed success.
Given the difficulty he had in doing this, I think that in a TL where the Commonwealth doesn't conquer Muscovy, Russia will probably gradually centralize around Muscovy or Tver or some other polity that throws off the Tatar yoke, but any state that develops organically like this will be much more decentralized than the Russian Empire and then later Republic have proven to be. After all, there is no ideological motivation this way. I doubt the Commonwealth would have been able to put a stop to it. Going Protestant made ruling over their Catholic and Orthodox subjects rather difficult at first, especially once the Holy Roman Emperors were able to start intriguing.