You _want_ people to check frequently; else qpopper must scan a large mail spool file, which is what causes this load. The best answer is to run qmail or postfix and use maildir instead of mbox. The performance difference often is astounding.
But the problem is that if they have a large mailbox due to mail-left-on-server and they check often, often they need to read the entire file. We spent hrs on this last week, getting rid of the big mailboxes of old messages was the key, when users check mail now it is about .4 seconds (that's point-4) so I could care less how often they do it. For us, it was the ones with mailboxes of 5-50 meg checking mail every 10 minutes even that was killing us.
Jale