Whenever one plays in a given game, it must be accepted that the universe in that game is going to be 'canon' for the duration of that game. When you then jump to another game whose authors disagreed with those who wrote the previous game, you will have to accept the new authors' version of that universe as 'canon' within that game, or you will make mistakes and generally be unsuccessful.
That's even supposing that an established canon exists, which in ST's case can be debatable. Are the Star Trek: Destiny novels canon? Then doesn't that invalidate any future appearance of the Borg as a threat to the Federation? What about Star Trek: Enterprise, where the Klingon homeworld is only a few hours away from Earth at Warp 5?
Bottom line: As long as you are playing in STO, STO is canon for you, and Star Trek: Legacy is not. When you go and play Star Trek: Legacy, then Star Trek: Legacy is canon, and STO isn't.