Well, I don't think you need to worry about that particular route. Generally speaking, if SkyEurope still operates by that time, then the flight will take place. Somehow. By someone.
Weather it's going to be an Air Slovakia, an MD80, a 737 NG or a 737 vintage is the surprise-factor. Could be anything.
Unless another plane gets chained up somewhere meanwhile, there should be a flight going. Don't expect too much from the on-time-performance, though; if there ever was one, there is no more guarantee for that anymore. You might find yourself waiting at either airport for a few hours now.
As long as you're not under time-pressure (and you even have a contingency-plan as you say), go for it.