I'm also experiencing exactly the same issue with deleted SMS messages showing up in the Spotlight search.
I've reported this in the Apple store 1st week in April so hopefully someone will be working on it.
The only way I have been able to clear the history is to wipe the entire phone, back to factory settings. Much quicker way right enough is to turn off Messages within Spotlight Search. This can be done by going to Settings - General - Spotlight Search - then untick Messages.
A few of my friends have exactly the same issue, all using exactly the same phone - iPhone 4 - 16Gb. However, some other friends using the iPhone 4 32Gb haven't encountered this problem at all, so it might be limited to the 16Gb model.
It would be useful to know what model everyone else has?
Here's a discussion I have found elsewhere - which goes into detail on how to backup and erase your phone.
http://forums.macrumors.com/showthread.php?t=1047576
Lets hope Apple fix this bug sooner rather than later 🙂