Bellisario commented on his micro-managing tendency on the NCIS Season One DVD. He said he'd overseen JAG for some time longer than expected, and was unsure about doing the same on NCIS, but Harmon was originally very eager to work with him, so he made the commitment.
Work environment aside, it's common for creators to leave established shows. I don't expect this to impact the quality much. Then again, those late script changes may have been improvements.
TVGuide.com asks if NCIS could survive without Harmon's character Leroy Jethro Gibbs. IMO, it could go for a while like X-Files, but the show is such that every character's role has impact and it wouldn't be the same show without Gibbs.
It sounds as if Bellisario is stepping away to increase the likelihood Harmon stays. Perhaps he doesn't want to risk an NCIS without Gibbs.