In the end, Clary found out about Alec and Magnus being together by accident. It was neither a kiss in the office or at a party, but the day after fashion week.
Alec and Magnus were lounging in bed having a relaxing morning after the events of the previous week. They were having a slow make-out session, enjoying each others company before they had to go back to real life and their demanding jobs. They were discussing having a vacation in between lazy kisses and feeding each other breakfast. They lost track of time until the door unexpectedly opened.
"Alec, have you seen Magnus? I went by his room earlier to tell him it was time to check out but he wasn't there. Oh, God!"
The sheet covering the boys slipped down as they turned towards Clary, showing off their nakedness. Clary covered her eyes.
"I'll just go." Clary closed the door behind her leaving two giggling boys in her wake.
"Not the way we wanted her to find out." Alec said to Magnus.
"Ah well. She was going to walk in on us sooner or later." Magnus laughed and went back to kissing Alec.