There are 3 ways to get rid of it:
1. Use the AR Max DUO to hack the seed out of your town.
2. Use a SuperCard/M3/some
GBA slot flashcart with eepinator or REIN to hack the gamesave to get rid of the seed.
3. Send your game into Nintendo and say that your game stopped working when someone came to your town, but don't mention that it was a hacked seed or anything.
Please note that options 1 and 2 are not supported by this forum or by Nintendo, and that if you ask for help with options 1/2, you probably will be breaking forum rules. I'm not even sure if I'm allowed to be telling you these 2 methods.
Anyways, I perhaps could help you ONLY if you are going to use my help to get rid of the seed. PM me, and I will ask an admin if I'm allowed to help you with that using gamehacking methods.
If I can't help, use option 1.
-SuperGeek
P.S. By any chance, do you know who seeded your town? Are they a Friendcodes.com member? If so, PM me their username.