Start deleting messages one at a time by long pressing and selecting delete? Will take forever to get it down to a manageable size... but oh well.. Or have you tried deleting the thread and just letting it sit? Like hit delete before you go to bed, then see if it worked in the morning..
install "sms quick delete". while in the app, select a thread, so u can see individual messages. press "select all" and then "delete". it will take a LONG time to delete them and will lag the phone until it is completely cleared. the app will continue to delete msgs in the background only when the phone is awake. you can see the progress in the stock messages app; the msg count will continue to diminish. do NOT allow your threads to exceed 500 messages or your phone will start to lag when sending messages within that thread. for some reason, android was coded to load ALL your messages within the thread thus making your phone lag.