As you say, deleting the programme itself isn't enough. Blocking the websites probably won't do much good either, because there are always just enough proxies to get around that sort of thing (and the Internet Explorer block is useless because it can be evaded by simply changing browser!)
I know you want to remove access to MSN completely, but this is just something to be aware of in case she manages to install it again: you can go to Control Panel\User Accounts and Family Safety\Parental Controls and set up a password-protected time limit on her MSN use. That could allow you to compromise as well.
Really, the best way to guarantee that she won't be able to access it is to make her give you the password, so that only you can sign in for her. Make sure her computer's sound is on (by default, there is a sound notification for everything and she would have to disable each one individually to stop it making a tremendous noise. 
)
Make sure she's working in a room with an adult and try to sit so that you can see her computer screen. You won't even have to waste time being the "MSN Police"; she's unlikely to try anything if she thinks she's being watched.
The Internet has an endless supply of distractions, so it might be easier if you can tackle the fundamental problem and get her to do her homework first, with the promise of MSN time afterwards. Otherwise, it'll be Youtube next. 
Good luck.
- a 16-year-old with inside knowledge of the various ways to avoid being blocked from MSN