Heya,
Well I asked on the FR mailing list, and as of today no WotC official answered my question. The mixed bag response seems to be...
Yes, no, and maybe.
The strongest argument why not: Because the Bhaalspawn wars aren't mentioned in the timeline in FRCS, and no one has said that they are canon.
The strongest argument why so: Because no one has said they aren't canon, and most Realms novels are concidered canon to the setting. (Which would mean Philip Athan's BG1 and BG2 novels, as well as the third ToB book (which wasn't by Athans, and I can't recall the author's name right now) would be canon, not the games)
The strongest maybe: Realms novels are canon, but for some reason this seems selective since the BG novel arc, Neverwinter Nights, the Icewind Dale Trilogy, and the Threat from the Sea novel arc seem to have been largely ignored in canon.
So, I can't prove a thing!