The is a reference to "Doom in Smash" thing. I feel old Doom perhaps could have a chance... but modern one is unapologetic about how gory it is.
The Doomslayer himself is not an issue, it's a guy in green armor with a shotgun, the issue is the rest of the game. Imagine some kid seeing Doomslayer in the game and deciding to check what his game is about. This is the kind of thing I believe crossed the mind of Sakurai when deciding if a character can get in or not.
Just for curiosity sake I decided to check Bayonetta trailer too and it's less explicit than I remembered. Sure you have some spread legs here and there but it's part of the trailer which also has angels, dancing and transformations.
Doom is RIP AND TEAR start to finish and if you remove it from Doom the game would lose a lot of it's identity.