Eileen's never believed any of Todd's previous warnings about Phelan! She's now in even further over her head having agreed to marry him, so I can't see her taking Todd's word over his this time either.
You should know that everyone in the Corrie universe (including the aptly-named plod) always takes the word of villains who smirk and twirl their moustaches at every given opportunity over their nearest and dearest.
I can't imagine how he's going to explain himself but - seeing as we know he's staying put for the moment - it appears he must come up with a credible story that satisfies Eileen and the police (at least in the short term). He did have a few hours after discovering Vinny's deceit to work something out and destroy any evidence against himself - and even perhaps manufacture evidence against Vinny (and maybe Todd too).