Can a plan allow a participant to pay off a deemed loan if the plan does not otherwise allow for after tax contributions?

Yes. The repayments on the deemed loan (if it has already been taken as income, that is) would be considered after-tax for basis purposes only. ("after-tax" contributions defined by your document are probably elective contributions tested under the ACP test....loan repayments are always after tax and do not depend on the document allowing for these types of contributions).

You'd have to keep track of this so you know what's actually taxable to the participant when they take a full distribution @ termination or retirement.

Vicki