"It's kind of hard to miss you when I hear about you daily," Jonathan muttered, standing to greet Joker. The man was one of the few he would bother wasting his manners on. "You caused quite a stir with your activities of late, Edward has gone over teh edge, he's even talking of turning you over to the heroes."
That was as close as he would come to actually saying Edward was ratting them out, but Joker wasn't an idiot and Jonathan trusted the man to catch the unsaid words. "Also, your toy has already healed herself and has been seen in the presence of the Black Canary."
Marcus was a font of information if you knew the right questions to ask, and Jonathan was nothing if not good at toying with people's minds. Hypnotism also helped.
Were Jonathan a normal man with normal human emotions...or any emotions really, he would feel bad about betraying the Nigma's. But he wasn't, and Joker had been his partner first. What he may or may not have felt for Edward had no bearing on who owned his loyalties. Especially when Joker offered him the Bat to play with and the possibility of him appearing, the needed fear Jonathan craved every second of the day.
Yes, Jonathan cared for Edward and enjoyed spending time with him...but he would take fear over lust any day of the week.
"I have your...gift secured downstairs. Scarecrow has been annoyed with you not retrieving it sooner."