Cylons being manipulated by other cylons doesn't absolve them of guilt.
BSG did have a few instances of the reverse of OP's question tho -- where the "good guys" turned out to be bad" -- trying to say this without spoilers; it's a 20 year old show but ffs of you haven't seen it, go see it now.
- the (temporary) new admiral
- several main characters during the part where they live on the dirty planet
- a very specific set of seven main characters (wink wink) ... .and more,..
And there's one specific example of the full 360 -- a character that starts good, turns bad, but turns out they were actually good all along. I won't give the name, but they were passing messages to the resistance.
That show was awesome.
One note tho, on the topic generally: flipping character alignments is a frequent pre-shark-jump thing, and is often bad writing. In BSG, tho, all of the "flips" are pre-planned, or at least 100% true to their character (eg the 360 example above).