Subtraction of utility's renewable energy sources from RECs?

If you are not purchasing qualified green power from that utility then the answer is as you have guessed. The renewable sources from the utility could be part of a government mandate like an RPS in that state and would not even qualify as Green-e sources. Often large scale hydro does not meet the Green-e requirements either.

I have a similar situation and it all started with the same question about "making-up" the difference and then I found out that it was not a qualified program, but the utility has a separate program that is green-e certified. They are telling me that by selling us renewable energy directly, (through this program) the REC's generated are retired by the consumer and therefore eligible for EAc6. I guess I was chasing REC's (which is actually the third approach to achieving this credit). What I have found is that certainly my client can purchase renewable energy however in this instance the cost of that energy is 10 times more than the cost of a 2 year REC contract with a separate provider. To me it seems like you can purchase the power and further the market or make a donation to support it through the purchase of REC's.

Both type of Green-e certified purchases serve to further the market for renewables. A direct utility program or a REC purchase can result in very similar market outcomes. There can often be differences however, and you may not be comparing apples-to-apples. RECs in general do tend to be cheaper to purchase. If all the client cares about is cost then the decision is pretty simple. If there is interest in a deeper understanding then the decision is not quite so simple. Many utility programs support more local wind or solar projects. RECs can be for other renewables (like landfill methane) that may be located in other parts of the country. You can get RECs that are more tailored to location and sources but they tend to cost more too. So if there is interest check the details on location and sources which will provide a better comparison. Personally I pay more for 100% wind RECs that are built in my region of the country because I want to directly support those projects.

Thanks so much Marcus, it is good to know that there are "in between" options - definitely worth investigating.