This is a cool problem.
I would try to do something consistent with how keepers have been "priced" in terms of draft picks up to this point.
One idea is to use the results of a 2012 auction re-draft from an experienced league with the same number of owners and roster spots as your league has and use that as a baseline for determining keeper values. Since I assume that keeper prices under your league's current rules are based on the round each player was picked, you could easily determine the average 2012 (and 2011, and 2010 and so on if necessary) auction cost of players in each round and use those numbers.
For example, let's say the average cost of the 10 or 12 guys taken in round 1 was $50 and the average cost of the round 2 picks was $35 and the average round 3 pick was $25. If your current rules state that a keeper costs the draft pick in the round he was taken last year, you could now say that keeping a guy drafted in round 1 is $50. If your current rules call for keepers getting one round more expensive each year they are kept, you could escalate the auction keeper price in a similar way. In that model I might use a flat increase ($5) instead of bumping up to the next round's price, but that's just personal preference.
I like that system better than the flat rate pricing because it enables more keeping of good sleeper draft picks. Just considering my own team under the flat rate model, it'd be awesome (but maybe unfairly cheap?) to keep Calvin Johnson for $5 and Arian Foster for $10 and then AJ Green for $15, but then I wouldn't be able to keep, say, David Wilson for $20. Whereas since Wilson was a $1 draft pick who might have been a 15th rounder in a snake draft, I should probably be able to hold onto him for a buck or two or six.
I think the main variable in figuring out how to make something like that work for your league is how far back the keepers go and how to use past years' auction data to assign fair prices to guys who have been kept for years. But again, I think the answer is to come up with something that values them fairly equivalently to how they are priced in the existing system.
Good luck - I love this question and if you want to discuss it further in this thread, I'm happy to participate.