I think they have clearly signalled since the start of Season 2 that they were echoing the story of RENT. The inclusion of Jesse and Daphne, the poster, hell, they even refered to Hit List being like RENT. Plus they have acknowledged it in interviews.
http://tvline.com/2013/05/04/smash-andy-mientus-kyle-dies-dead-interview/ I really don't see the issue with this at all, as has been pointed out this kind of thing is done all the time in movies and tv, why should it be any different here.
Personlly I think it has been a great homage to RENT and Johnathan Larson. I have loved noticing all the little RENT references throughout. And I think its great that it might bring the story of JL and RENT to people who didn't know it or remind them of it. As a result of the show I have spent time looking at RENT clips on YT and listening to the soundtrack, something I haven't done in a long time. I also told the story of JL to my niece who didn't know of it. So I really don't see the issue with it. Presumably Jesse L Martin and Daphne Rubin Vega knew where the story was going and didn't have issue with it. I gotta say when Jesse was talking to Derek about whether the show should go ahead and he said it should to honour Kyle that brought a tear to my eye (yes, I am a sap!) as he must have been through that for JL.
I think Derek said they could use the music stands to help Sam....plus it looked good, so why not!! :)