If they're creating a workaround for the contested parts, it may delay the JB update, yes. If you're concerned that they will no longer push updates to our phones, I wouldn't be.
There's no need to flash a new ROM unless you really want to.
I lost root going to it, and am struggling to get it back...
EDIT apologies, using the rootkit below, I was able to get it back, just had to set the Phone version (in the root tool) back to 4.0.4 (I thought to try Custom ROM instead, since I thought that best described what I was running :/ inexperience rears its head!)