GURPS Pact Magic - another alternative system
"Everytime I died, I crossed over, and little more of the master came back with me."—Grigori Yefimovich Rasputin
GURPS default magic system has spells being powered from the wizard's internal, physical energy. RPM magic has the energy being gathered from ambient mana and possibly supplemented by the wizard's own internal reserves, at the expense of being rather slow.
Neither of these systems does much to model the character who is remarkably powerful, far beyond his own energy reserves, who can work literal miracles - but who pays the price for doing so in more permanent ways. Black magic that taints the soul, necromancy leading to eventual undead status, drawing on the powers of the Elder Gods at the risk of personal insanity, the Dark Side of the Force: all of these are represented as a sort of slippery slope, with practitioners starting down the gentle incline, testing to see just how far they can go before they can get back, sometimes returning changed for the risk.
Threshold-Limited magic (Thaumatology, p.76) takes a few steps in this direction, but with a fairly limited scope. Energy can be pulled from whatever source, but when you go beyond a certain safe point, you run the risk of temporary power loss, gaining disadvantages or losing advantages, which sounds like we're on the right path. But there's no long-term impacts in terms of the slippery slope. Abuse your magic, start to grow tentacles on your back, rest up a while and then start over again - sure, the tentacles are there still, but you're no more likely to overreach than you were last time. There's no lasting stain on your record to make the next step more likely.
I'm going to suggest a slightly different model, based very closely on Threshold magic, where in addition to your Threshold (the amount of magic energy you can safely use before you run any risks) and Recovery (the speed with which your tally drops over time), there's a third figure that is directly involved in your penalty on the roll for Calamities. It will be set by your abuse of your power, and while it will return to zero eventually, it will take a long time - significantly longer than your normal tally does.
This third figure, let's call it Corruption, starts out at zero just like the tally used to track your use of magic. It only increases if you exceed your Threshold, and it goes up by 1 for every five points by which you exceed your Threshold, modeling the same results as the standard Threshold magic rules. The difference is that your Corruption value drops by 1 point per week that you go without using any magic at all. So instead of the penalty to your roll being always based on the severity with which you have overstepped, it is based on a long-term calculation of your level of abuse of your powers. Take a month off from using magic and it'll drop by 4 points. Keep using your magic, even a little, and it'll stay there, a taint on your soul, or a susceptibility to insanity or your first steps on the path to the Dark side.
This might need to be tweaked a bit to model some fictional magic systems, and really specific Calamity tables would need to be cooked up for each of the pacts that are valid in your game, but otherwise it could be a very flavorful addition to a world where magic is dark and treacherous, even in the hands of the righteous.