I'm not so sure about that.
I think it would ruin the mood of both.
I mean, for the minbari the humans were primitive murderers or even monsters deserving nothing but extermination.
And the humans saw the minbari as pretty much the same as the minbari saw the humans.
Now if you switch around all the time, it's hard to really feel like your the good guys and they are the bad guys.
Even if you start out with a minbari completely into the "holy war" and slowly coming to understand that they are wrong would be better to have in it's own campaign I think.