But, to answer your question, no there is no alternative mail app that will do what you want. Well, at least not one for a generic POP account. You might find something for GMail or Yahoo. We are all waiting to for some developer to turn out a full(er) featured mail app for the iPad, but nothing yet.
Some new features for the Mail app are coming this fall in iOS 5, but I don't know if improved select and delete are part of it.
If your mail account has a web site, then try visiting it using Safari. Many of these sites work fairly well on the iPad. This should work (well enough) for those time you need to delete bulk amounts of email.