You can only remove the second Gmail account that was setup. Once its removed from the phone, its also removed from the Market. You will not lose any downloaded apps but you will also have no way of updating them in the future unless the account is added back to the phone.
You can not delete the primary Gmail account. That's the one that's used when setting up the phone for the first time. Its also tied to the Android Market so you can't remove it from there either.... UNLESS, you're phone is rooted. Then you can delete the primary account.
The only way to remove the primary account (unless rooted) is to factory reset the phone. Then when setting up the phone again... you would change to a different email address.
If you have any other questions... feel free to ask.