I'm also a big fan of RockAuto (BTW, google for a 5% off coupon code; they will send you one after every order and it expires in a few months, but people post them to all kinds of forums, so you can always find one).
That said, I don't blame a mechanic who won't install parts you carry in. What if you buy the wrong part or there's a defect with the part you buy? They deal with a local warehouse who will deliver parts to them, usually multiple times per day. They don't want your car half apart, the wrong or damaged water pump, and a multiple day wait while you chase down the issue. I don't bring my own beef into McDs, and I don't bring my own parts to a shop. You'll find someone on Craigslist who will be willing to install your parts, but I doubt you'll find a good shop willing to do so.
You pay some markup on parts and that's OK in my book.
A timing belt and waterpump job is moderately ambitious for a first-timer, but if you follow along with the service manual, you should be OK.
My advice is:
1. Never work under a car supported by a jack! Buy jackstands and give the car a good jiggle once it's up on the stands.
2. Never work on a car without an alternate source of transportation to the parts store. I've had to ride my bike to the parts store to get myself out of a jam. When you're just starting out, you have a higher chance of needing some random tool that you don't already have.
3. Make sure you know what gaskets/O-rings are involved in the water pump job and make sure you know what sealants to use on them. Doing a big job like this and ending up with a leaker is a royal PITA!
4. When there are choices of waterpumps and you can buy either the "working half" of the waterpump or a whole waterpump, always buy the whole waterpump. It's not worth field servicing them. (This was common on early watercooled VWs; not sure about your GF's car.)
5. I wouldn't sweat the timing belt hard just yet. Yes, they do eventually break and if yours does, the car might be totalled (as a junkyard engine R&R is more than it's worth), but in all likelihood, you can drive the car another 25K miles without issue. (No guarantee, but don't feel like your hair is on fire and you must change the timing belt before the next summer. It's a risk, but a very small one, IMO.)
6. I would always change the water pump if doing the timing belt, not so if just doing the external belts.
7. Counsel your GF that if she sees the red battery/alternator light turn on, she should park the car as soon as it's safe to do so. That is often a broken belt, and often means no water pump. I've seen people "know" they wouldn't run down the battery and keep driving, cooking the engine because, "it's just the battery light".