I really love the non-Militant sisters in BoM. One day, I'll get to to play a Sister Famulous…

 I think it depends on the type campaign your gm runs, if they run a predominantly combat orrianted one bom is better suited IMO, where as for investigation the inquisitors handbook is better. 

As a side note the faith powers in bom are very very good

Well for me it's clear cut.

The original Sororitas rules in the Inquisitor's Handbook, in their efforts to make every type of sister workable in a single career package, pretty much failed entirely. It created massively broken Battle Sisters with no weak stat progressions who were all-powerful godesses at almost anything they attempted. On the other hand the Diologous and Hospitaler were lukewarm at best for their intended purposes, not to mention the absence of rules for the Order Famulos, who are quite probably the most interesting of the Orders to begin with.

The newer and better thought out rules in Blood of Martyrs provide proper rules, fairly accurate lore and good signature equipment for all three of the non-militant orders. Furthermore, the updated Battle Sisters are not only of a more reasonable (though still noticeably higher) power level than other Dark Heresy careers, but they gain free and legitimate access to their signature equipment.

Sure, you'll be walking into a hell of a lot more ambushes if your Battle Sister, or anyone else, for that matter, is silly enough to parade around in their Power Armour during an investigation, but at least she has it when the time comes to break out the good stuff and go loud.

I'm not saying it's balanced against the other careers, of course, but it's better designed and overall way, way more reasonable. Between the greater selection of Soroitas-only abilities, sacred gear, faith talents and extra lore to call on, it just plain works cooler, smoother and better than the busted-as-hell mishmash in the Inquisitor's Handbook.