Right up until the point she produced the Sonic Screwdriver, I'd have said there was little in her manner to differentiate her behaviour from other companions he's been particularly close to (beyond the fact she's clearly making assumptions about multiple out-of-order meetings and therefore a long-term relationship of some sort) especially when you factor in New Who's more touchy-feely approach to the way these relationships are presented.

To be honest I actually think it was a mistep on Moffat's part. He wanted to make sure the audience understood what was going on and, for once, rather under-estimated our ability to keep up. But the effect was that both the Doctor, and River to be honest, looked a little slow on the uptake.