Seeing how the fandom was already ready to boycott ENT before anything was known about it in the least, I don't see how this theory is all that outlandish. By the time ENT came around the fandom had become a hatedom, for the dumbest reasons.
I was around at the time, and yes ENT recieved buckets of scorn, and part of me misses that because the ENT forum tends to be a lot more pro-ENT these days... which is because, again, the people who like something are the ones who still care about it in the long run. Anti-ENT fans only cared about ENT when it was the new
Star Trek, they've shifted their attentions, positive or negative, to the Abrams film.
But Niners embraced nuBSG because it was the sort of show they liked. If ENT 'ripped off' B5 and did so in a way they
didn't like, they'd criticize it.
This is the double standard of relevance. It may be Niners may bash something they dislike by accusing it of things that could be fairly levelled at something they like - but you're assuming they'd automatically dislike it, which seems untenable. I think it'd be fair to say there are more than a few Niners who enjoyed ENT's fourth season, for instance, and a fifth would probably have been much like the fourth in tone and style.