The margin may be better for Silver's, but I doubt it for any of the other levels. Assuming DL is getting .01/mile from AMEX, the waiver is only generating $250 for DL. Plus it adds a liability of 25K miles (or more) to the books. I believe the waiver is likely due to the total value of the AMEX relationship and has little to do with the amount of income it actually generates from individual Medallions. Given that DL and AMEX just recently renewed their relationship, I'm going to bet that AMEX has contractually embedded the MQD waiver and agree that it is unlikely to go away.
In making the comparison, you should also ask what profit margin DL earns when a FO spends $2500 on airfares that qualify for MQDs. I very much doubt that it's 10% (consistently) on fares that average ten cents per mile.