If only it were that simple!

Modest will always index all your subscribed personal folders, so if you have even one folder with lots of messages somewhere in your tree you'll still hit the problem (bug 3762).

Unsubscribing that folder (which you may not want to do in the first place if you want to access it from certain other MUAs) may not help either, as Modest sometimes (depending on the IMAP server) will ignore IMAP subscriptions and fetch the entire personal folder tree (bug 3484).