If an EE has made after-tax EE contributions to a QRP in which he/she also has pre-tax benefits, may he/she withdraw just the after-tax EE contributions (and not be taxed due to the basis), leaving the pre-tax benefits and investment earnings in the QRP for later withdrawal? or are any withdrawals deemed to be proportional between the after-tax employee contributions and pre-tax benefits, with just a proportional amount of the basis applying?

Proportional except in circumstances dealing with pre 1987 amounts. I won't go into the details on those as they are rarely relevant today.

If the employee is eligible to withdraw the entire account balance because he is 5 9 1/2, why cant he do a direct rollover to an IRA and then roll the pre tax amounts back to the retirement plan leaving only the AT money in the IRA which can be withdrawn without penalty?

Going back to the original question, depends if you mean DB or DC. QRP can be an inexact acronym.

DB -- the ones I've worked with had provisions that the employee could withdraw their contributions but would lose any associated benefit making it a very costly withdrawal

DC -- depends on the plan's provisions. It is possible to have a withdrawal solely of after-tax monies (proportional between contributions and earnings).