Fugliness

Without wanting to be called Captain Obvious, and without knowing the table structure, it looks like some serious indexing is needed - presumably there's some kind of ThreadId along with a PageId? A multipart index on those two - PageId first - would be my guess. But yes, profiling is the way to go. Actually, it already seems quicker than it was earlier.

I think the bottleneck is in the parser though, at least that's my experience with wigo, which has a similar problem performance-wise (lot's of small, separate pieces of wikitext)

I know you know more about MW than I do, so I shall defer to your better knowledge... but as a SQL DBA I would still suggest a quick look at the indexing.