I think you can maybe get away with Cena not being at Raw tonight. It's not ideal, but you can build the show around people acting shocked at what happened - focus promos, backstage vignettes, etc on people trying to process what happened. Kinda similar to how WCW had various wrestlers discussing Hogan's heel turn on the July 8 Nitro (although Hogan was at that show, from memory he came out at the end for a promo). Let the indignation, shock, disappointment, etc really build to the next show.
However, if Cena is away for multiple weeks then it severely dilutes the whole thing. We aren't even that far away from WM so every week without Cena being there is a week wasted. If they wanted to turn Cena heel then it should be an all-in commitment from both sides. If that isn't possible, then just don't do it.
If you think about Hogan's heel turn - he was a face in WCW for roughly 2 years, from mid-1994 to mid-1996. The writing was on the wall, fans had turned on him (although not as viciously as they did with Cena) and so he did the logical thing and turned heel. Cena turned face around 2004/2005ish, and much like Hogan got turned on by fans quite quickly, but it took them 20 years to do a heel turn, despite constant and overwhelming rejection of his face role (up until very recently, anyway).
Imagine WCW kept going, but they also didn't turn Hogan heel at BotB '96. Imagine them waiting until 2015 before turning Hogan heel, during his final retirement year no less. Putting aside age differences and such (you have to de-age Hogan a bit for this scenario to work), that sounds absolutely ridiculous. To have pushed good guy Hulk Hogan for 20 years despite the fans not wanting it - and having him repeatedly win world titles and dominate during a significant portion of that time. Then finally turn him heel when his career is essentially over, having resisted the opportunity to turn him heel countless times in the past. It sounds like total insanity. That's basically what WWE have done with Cena. It's obviously Vince's fault this happened and Cena probably would have remained a face until the bitter end if Vince was still there, but man, it's just so stupid when you really think about it.