It is entirely optional. No great harm will come from waiting, but at the same time there's no compelling reason to wait either. If you decide to stop it now, there will be a brief period of unrest but he will quickly adapt. In one sense, the sooner he's able to cease his reliance on it for sleep the better.
You are sort of on the right track at bedtime, but you are not following through entirely. Your wife has to stop 'using' herself to put your son to sleep. This is only compunding the problem. The hour or so of crying isn't so bad, under the circumstances. Instead of resuming use of the pacifier, I would concentrate on eliminating the behavior of your wife's deferring to your son's crying.
We stopped giving our now 20 month old son his paci at bedtime back in late Feb. He's still having a hard time with the transition, basically using my wife as a paci to put himself to sleep before bed. If he doesn't fall asleep while breastfeeding, then he stands up in the crib and cries hysterically. We have been trying the "cry it out" method, where I go into his room every 15-20 minutes until he falls asleep, but sometimes he's still crying after an hour and my wife ends up going back in to put him to sleep. Compounding our problem is that my wife is trying to wean him off breastfeeding, but given that he's using her for a paci, we don't see that happening any time soon. Additionally, he is not responding to me (the father) during bedtime at all. He just wants my wife to rock him to sleep.
My question is, would it make any sense to start giving him the paci back, just at night? We've been thinking about doing this over the past couple weeks. Basically, it would be no paci during the day, just at bedtime. We don't want to confuse him by re-introducing it now, or make it harder to get rid of it down the road, but we're not sure what other options we should consider at this point. Just curious as to what your thoughts are on this.