Eobard didn't know how to handle this situation. Gratitude through physical contact, especially intense contact to this degree, but the emotions were too difficult to deny. Primarily because he didn't really know entirely how to react to them, so he just went with what Hartley seemed to think was appropriate.
And besides, the deeper he pulled the other man into this, the more satisfying it would be when the others found out. After all. It was unlikely they'd be able to convince Hartley that this was nothing more than a manipulation if he fell even slightly as hard as he had before.