btw has RDM ever been called out on it ?
on the other hand I can accept the fact that Baltar wasn't too keen on testing people & wanted to bury his ehad in the sand if we take into account the fact that he was as you said "confused" about the cylons (not to mention the fact he was completely bewitched by Head6 - and who wouldn't be -)
but Boomer was a different story, he already knew what she was : a walking timebomb that could go off any time. he had every reason to turn her in, other cylons going after him was less of a problem knowing he could get a security detachment to guard him 24/7 (wouldn't have upset his life much as he was already spending all his time cooped up in a lab anyway) especially since his prototype detector worked like a miracle (incidentally they dumbed down its efficiency in the following episode, another inconsistency looks like)
btw when interrogating Boomer he said he withheld Boomer's true nature from the rest of the fleet "for his own purposes" (whatever the hell these were ) which means that fear was not the reason behind his actions (or lack thereof) when it came to Boomer