My profile is used frequently with my JTAG and all my 360's that use Xbox Live and I have never run into any problems. I'm not saying it's 100% safe to do so but for me it's never been a problem, and I've used homebrew with the profile signed in.
The one thing that is a big no-no is playing homebrew games that have their own achievements. I believe I read somewhere that when MS sees the homebrew achievements it's an insta-ban.
If I were you I'd just go over your achievements and games played, remove anything like XEX menu, then BACKUP your profile using usbXtafGUI, and start using it on your Live console. I can't see MS banning the console for stuff that your profile has done on another Xbox, but I can see them banning your profile, in which case you have a backup that you can always put back on your JTAG and use.