The usual thing would be to grind or dig out the stumps and leave the roots to decompose where they are. Don't see how doing more than grinding the stumps out would cost less than just grinding the stumps out. How many stump grinding services did you talk to? Maybe you called one or two expensive ones and you can get it done more cheaply by several others. Often with all types of contracting those not thinking they need a particular job at the moment or that it might be a pain at any time will give a high estimate, figuring if they win the job they don't really need or want the extra compensation will be just that.

Or maybe you talked to outfits that only have truck-mounted rigs that always require a certain minimum fee. Here the work (stump grinding) may be done by a tree service, them perhaps going and renting a hand-operated stump grinder as needed if they aren't keeping one on hand. For less than enormous stumps such a machine may not be much bigger than a rotary tiller.

If you have a big project whoever you call is going to want to be paid enough to do the whole thing. To get a feel for what is fair market value talk to multiple services/contractors. Watch out for buried utilities if you start digging up roots, anyone doing this for you should have liability insurance adequate to pay for any surprises.