Jordan, I think that is a fantastic way to run an OP tourney. They aren't meant to be super competitive in the first place, so nobody will complain about the pre-matched pairs. Overall, given the current floor rules, I think that's a good mix of being friendly to new players and also keeping it at last somewhat competitive.
Really, though, with OP kits you should just be doing whatever your particular crowd thinks is best - I'm sure they were meant to be pretty flexible. But when it comes to the Sheriff/Outlaw/Marshal tournament, that model clearly doesn't work quite the same. What to do in those cases?
In a related tangent, I played in an OP tourney this weekend, using the blessed deck I've been tuning on and off since Tolarios was introduced. I went to time in 2/3 of my games. One was just a game that was a little slow paced, but overall just didn't see much action one way or the other. The other was against a less experienced player, so naturally things will go slower. At the very end of that game all I wanted to do for the last 5 minutes was simply move a guy from my home to an adjacent deed, then call out her dude. That whole time I was able to move my dude, and that's it.
It just really highlights the frustration of not getting at least ONE action after a slow opponent runs out the clock. In this case I really did not care as it was a very casual OP tournament, and I was actually really happy when we counted the totals and she won ("maybe she'll come back for more" I thought!) but, for the purpose of this discussion, I had no chance to react. If you are slow and you run out the clock, you block your opponent from any action. That's far worse than getting the final action and somehow sneaking in a last second victory. Chances are that time will be called during the slow players turn (not always, of course, but odds are with that), so it's only fair to give the other person one last chance to react.
Basically at this point I never want to play (in a more serious tournament) blessed, gadgets, or any other deck that takes time to build up before going for the win. The 5-3-0 penalty for winning at time is just too steep and too likely to happen even if both players play at a moderate pace. Like bithlord mentioned, it's better to go 2-1 before time than 3-0 at time.
This sort of point system will likely be largely inconsequential with tournaments of 8-16 people, since there aren't a lot of rounds (and thus your chances of playing multiple slow/newer folks or having a very close game are lower). So maybe this is largely inconsequential, but for larger tournaments I bet over time there would be a very heavy leaning to the decks that are geared toward turn 1 shootouts and town square camping.
Maybe I'm just particularly unlucky with games going to time. I'm definitely far from a slow player and I don't play slide, fortress, or showboating type decks, so I don't know. I hope if there is a higher level competitive series, like the Outlaw, that we can keep track of which & how many games go to time to see how (or if) it affects things. I just fear that with the 5-3-0 floor rules that we might be throwing a whole bunch of decks under the bus along with the pure slide/showboating/stalling decks.