My two cents, I don't believe wild yeast and bacteria are the bogeyman that a lot of people make them out to be. Wild yeast and bacteria are all around us, on us, in our homes, on our countertops on, on our brewing equipment (unless it's fresh out of the sanitizing solution). I think the words of warnings about not mixing"infected" equipment with clean beers came about because you have to account for the lowest common denominator...the brewer that does a lousy job of cleaning and sanitizing.
I brew both clean and wild beers using a lot of the same equipment and have yet to experience cross contamination in a clean beer. The only time I can think of where I had an unintended infection (as opposed to an intentional sour) was from some poorly sanitized peaches and apricots I used in a fruit beer. That said, you have to use common sense. For example, I can't take a bottling wand apart, so I use separate ones for clean and sour beers. Same with auto-siphons, I can't take them apart (and they have a tendency to form small cracks after time) so I have separate ones for clean and wild. I also clean and sanitize all my cold side equipment before and after use. If I put a sour beer in a keg, I totally disassemble the keg after it kicks and I'll usually steam the parts (posts and dip tubes) in a stream basket before reassembling.
My advice, heat is your best bet if the fermenter will tolerate pasteurizing temps. If it will, fill it with hot water at the proper temp for the prescribed amount of time. This link can help with determining proper temp and time
http://www.engineeringtoolbox.com/pasteurization-methods-temperatures-d_1642.html.
If it can't tolerate pasteurizing temps, I'd hit it with a multiple sanitizers mixed at greater than no-rinse concentrations. The idea here is you may come across something that is more resistant to one type of sanitizer than another, by hitting it with multiple sanitizers (one at a time) helps ensure you kill off as much as possible. For example, clean well then hit it with a bleach solution. Rinse well, then hit it with a concentrated Iodophor solution. Rinse well then hit it with a concentrated Star San solution. If it were me, is probably let it sit on each solution for minimum 20 minutes. Ok, I'll get off my infected soapbox now.