I was playing as a Lvl 6 Seneschal up until his head was blown off. Happens.

Mechanically as the player I'm really digging Missionary as my next character except that the story has been very supportive of Xenos. I know next to nothing on lore and everything I've found thus far says that I'd have to upon taking two steps on my "former" RT Captain's ship see it all be cleansed with fire. Not just lesser races but exotic xenos have been made pacts with.

I can always try another career choice but either in lore or home brewed is there some way to justify being supportive (and not back stab) to my Seneshal's former companions?

Well, the Emperor made Rogue Traders and allowed them to deal with Xenos, he had his reasons. But, be vigilant about their tricks and influence.

Also, there's other fish to fry on a Warp-traveling ship. Blessing people as well as weapons and ammunition is always good idea, and all that.