Could my idea of an independent Ukraine work with them allying with Prussia and/or Sweden due to being fertile land surround by empires each laying a claim to it?
Bohdan Khmelnytsky allied with Protestant Transylvania, the Radziwills, and Sweden against Poland in the 1650s in the treaty of Radnot.
The PLC would have been partitioned between protestant and Orthodox powers. In Ukraine Protestant nobles either fled to Poland, eventually converting to Catholicism for the most part, or remained and converted to Orthodoxy, see Yuri Nemyrych. So, political and military cooperation was quite typical.
Theologically though the protestants are "worse" than the Catholics from the Orthodox perspective. They are essentially outright heretical. Considering that the two most popular forms of protestantism in eastern Europe were Calvinism and Unitarianism/Arianism/Socinianism that makes things even worse, because the Lutherans are "wronger" catholics, the radical protestants are downright heretical and blasphemous. Calvinism feels like the polar opposite of Orthodoxy frankly.
Now, could a different Protestant movement align with the Orthodox? In the PLC Nemyrych tried to engineer a Unitarian "return" to the Greek Church as it was then called, this wasn't particularly popular and the authenticity of his conversion has been consistently called into question. Maybe if there was an Orthodox power further west than Muscovy, it could take advantage of the early protestant reformation to try and engineer a western rite orthodox movement out of a branch of protestantism. That would be interesting, but would require many early PoDs.