I tried something along the lines of this although I removed from the Blades Recruits faction. This resulted in them stopping the Blades talk but they continued to reside in Sky Haven Temple.
I think that their part of the SkyHaven faction rather than the Jorrvaskr Sleeping Quarters faction. Do you know if these are factions and if so what are their ID's!
*Take note of Lyn1964's command line*
I could not find any factions like you described, at least not using the same means that I came up with the Blades faction - you can download the Creation Kit (it's free) and dig around yourself, if you're so inclined. My gut feeling here is that there are a bunch of variables and game settings involved that you'd need some serious work to reset everything necessary to completely undo what's been done in-game. So, be prepared to accept your fate, as such.
Beyond that, the only other suggestion I have is to use the console to relocate the NPCs to Jorrvaskr: take the PC there, then open the console and use "prid (NPC ref ID#)" followed by "moveto player" and then "resetai" and/or "recycleactor" - again, you're experimenting around here and I cannot vouch for the efficacy of my suggestions - I'm just throwing some stuff out there and maybe you'll get lucky.