Even after last night, I will actually say yes. To me, its not about how they actually played in the bowl game b/c you can never predict that. You have to look at what the situation was at the end of the regular season.
And at the end of the regular season it was them or WVU. Both 10-2 teams. One had 2 losses against a pair of top-10 teams. The other lost to Louisville (who's good, but not as good as either of the 2 teams ND lost to, imo) and USF. As far as greatest quality win, WVU's were Rutgers (at home), Georgia Tech (at home), and I guess Cincinatti (at home). ND's were G. Tech (@ Tech), PSU (at home), and UCLA (at home-and remember, when the selections were made that was a UCLA team that'd just beaten USC). I think there's a slight edge there in terms of quality wins in favor of ND, they had the same record as previously alluded to, ND's losses were against better teams, and ND's Sagarin SOS overall was much higher than WVU's.
All-in-all I just think ND had the better regular season. If you want to make an arguement that Slaton & White could've done more based on what Walker did, that's fine, but to me who belongs where isn't about that. Teams to me should get in based on what they actually did in the regular season, not who has what players, or who is percieved as "better" despite similar or worse records, who is percieved as being able to be more "competitive" in the game. If you're gonna do that, then throw out conference tie-ins, b/c I can name a few teams I think were better that OU or Wake Forest this year that weren't playing in BCS games.
So yeah, ND to me "deserved" to be there, in the sense that they were the best of what was left in this year's BCS. If the system allowed for 3 teams from a conference to get in, then I might've felt differently, but it doesn't.