understandable call.
Statistically, you have a better shot of losing on a FG and a TD/2pt conversion than losing on a muffed PAT that is taken back for 2 and a TD/2pt conversion....but only if there is enough time for the opponent to have two possessions. Under a minute as they were, that's not likely to happen.
If you have more than a minute and the other team has multiple TOs remaining, you kick it.