Consolidators already do this from my experience in the UK and Australia. They'll add 3% when paid by credit card, more for Diners or AMEX. For that matter at least one discount airline (Virgin Express) does this too.
I would have thought if the airlines wanted to do this, it would be passed on to the passenger (and therefore the agent) by way of another FEE/TAX. No idea how hard that would be to implement, but the cost ought to compare favourably with the revenue brought in.
- Simon