You are correct - the wood floor is going to much more dimensionally unstable than the concrete and will thus "move" more, making a rigid floor spanning over the two different materials more likely to fail.
You could cantilever the new floor over the den slab by installing 2"x6" joists glued and nailed to the existing joists - make sure the new joists extend at least 48" (3x the cantilever) into the existing floor. This way you're not really bearing on the concrete slab so any movement that occurs will be consistent.
Also, if you're still leaning towards bearing on the slab, you definitely should use a treated lumber plate - preferrably either SBX (Sodium Borate - blueish in color) or MicroPro (natural color) treated wood. They are more dimensionally stable and true than ACQ treated lumber.
If you'd like more detail on the cantilever idea feel free to email me at
design_tech@windstream.net. Good Luck!