Do you think having Unity would mess with shell?
I ask this because I already have had the issue of the unity global menu appearing behind the gnome panel.
I have resolved it, however do you think that there could possibly be other bugs caused by presence of both DE?
Assuming you are using 11.10, the answer is
NO.
The reason why is extremely complex, but to simplify it, removing
Unity
will break your system upgrades, and make it extremely difficult to get security updates for some parts of the Ubuntu Desktop.