If I recall correctly he was mostly halo-ing Murph, right? And she was in full-on-angel-possession-mode? I think it’s likely that if anyone saw it they’d assume it was angelic presence, and I don’t think anyone tipped wise to Bob.
And if any of the Grey Council had engaged Bob during the fighting with Kemmler, they'd be familiar with the blue Evil Bob, doing a whole lot more actively destructive stuff. Drastically changing tactics with the removed memories and glowing a different colour is a decent casual disguise ... even if most of them recognized Harry's squad had a spirit being helping them, the don't have reason to connect that it's /that/ spirit being.
Now, on the general topic of things that make Harry scary, it's yet to pan out, but his "they're looking now; let them find something positive" strategy seems to be about laying groundwork toward eventual contact with the vanilla authorities. I don't doubt the Librarians are going to be somewhere between inconvenient and antagonistic for a while, because, hey, it's Jim writing this. But longer term, when they're ready to reach out to someone to make contact with, the monster-slayer who advertised in the Yellow Pages is probably going to look better than supernatural nations they're starting to see the outlines of but are trying to hide. In practical terms, good relations with the mundane authorities would actually be more useful in a lot of ways than something like the ability to let horrors out of Demonreach.
If you think the Council is pissed and frightened now, just imagine the apoplexy if, around about book 19 or 20, Harry is leveling up from consultant to SI to consultant to Interpol and the UN security council. You want to kill the guy who's talking to the mortals about how to protect themselves from another supernatural attack? Enjoy your new #1 spot on the list of things they think they have to protect themselves from.
At this point I really want to see Ramirez drop by to spot-check Harry's conduct, and barge in on Harry hosting some feds he's on good terms with for a chat. Explaining that one of the secretive nations has someone under a suspended death sentence for going too far in defending Chicago would be a /great/ look for the Council in front of mortal authorities.