The reason that the doctor told you it's unsafe to continue using Depo-provera for a long period of time is because the FDA has placed a "black-box" warning on the drug, because it's been proven to negatively affect bone density, thus giving women who use it for an extended period of time an increased chance of acquiring Osteoporosis. My doctor said that, two years is the FDA's fallback - so that they can't be sued, just in case. She believes the limit, essentially, is more about four to five years.
It's not the symptoms your doctor is warning you about. The only reason the symptoms are so much more pronounced is because it's a high dose of hormones all at once, rather than a little bit every day (like the pill, for example). Your heightened symptoms aren't dangerous to your health, though I'll admit they can get very annoying.
Not that I'm trying to advertise for Depo or anything, but I find it to be a very safe form of birth control. The symptoms are usually pretty bad in the beginning, but mine have all but subsided. Sometimes, it just takes time. Your body needs to get used to all those hormones.
I guess it depends on the person, though. Either way, good luck with your hunt.