I haven't personally removed the weird bit (Tyranid plant) from my Zoanthropes, but I thought about it. I think that removing it will be easy the problem you will have is sticking the Zoanthrope securely to it's base. Because a Zoanthrope is quite top-heavy it will be likely to break off the base.
I think what you will need to do is pin the Zoanthrope to the base. You will need to squish some green stuff/putty/milliput on the underside of it's base. This is needed so that the pin you use will be more secure. The problem you will have is that there won't be much room for you to drill a hole for the pin to go into. This means the pin won't be very strong and will be vunerable to breaking. Basically you need to go right up inside it's tail to make the grip on it's base strong. Take a look at this image of my Zoanthropes and it is easy to see how difficult it may be to drill a good deep hole.
Image of Zoanthropes - Photobucket - Video and Image Hosting
I personally would suggest you either learn to like that Tyranid plant or you cover it up. You could use some green stuff to cover it. Once the Zoanthrope is trimmed and so on glue it to the base as normal. Then you can try to use green stuff to cover up the plant. You should probably put rocks on the green stuff or generally cover it with sand etc.