Should I deal with the pain or wait it out?

Are you having actual pain or just muscle soreness?

Muscle soreness - ice/heat, stretching, ibuprofen (or your preferred pain reducer) and light exercise.

Joint/tendon/ligament pain - see your doctor

Two things here: 1) you should be giving your "worked" muscle groups a resting period and 2) the EXTENT of the pain is the question: is the pain from injury/overwork or just lactic acid buildup? If it's the latter, try stretching before/after exercise (and do a good warmup before strength training. Most fitness experts are now suggesting a minimum 5 minute warmup on bike or elliptical instead of just "static" stretches. See http://www.bodybuilding.com/fun/how-bodybuilders-can-avoid-tendon-trouble.html).

It's awesome to be motivated but be careful to not push it and put yourself out of the game.

Pain and soreness are two very different things and it sounds like you're talking about soreness.

It's natural to be sore after a workout. Cool downs, stretching, and rest are the best ways to deal with that. Assuming you're doing all three of those, then it's fine to use protein, potassium, and anti-inflammatories to promote muscle regeneration and reduce discomfort. I used to use protein shakes or bars after a work out. I prefer naproxen sodium (brand name Aleve) as an anti-inflammatory. Remember that overuse can damage your liver so you want to take as few as you can (one after a workout is usually enough).

As always, consult your doctor before you try anything and make sure you let him or her know what pills and supplements you are taking every visit.