If you got merit for a post, you won't lose it, and it doesn't matter if the post or the thread in which its in gets deleted.  That's one of the things I like about the merit system--it's permanent.  You can lose activity and posts, but you cannot lose merits once received.
And Theymos doesn't really want much action against merit abusers, since in time they should burn themselves out.  The way sMerits decay when they're given out kind of ensures that.  Yes, some people are going to rank up who shouldn't, but it's still orders of magnitude better than before.