From an in game perspective, what is the best way to fight against mages?

Funny, because that's what happens to a mage in comic: mage killer. They did all the right thing that people said in previous posts and killed the mage asap, but she eventually became possessed.

abomination killing is a different matter and have it's own proceedings

Well if you don't have magic of any sort, and if you don't have plot armor, the ideal answer would probably be "don't." Run away, hide, surrender, find the nearest templars or less hostile mage, whatever. Just don't fight the mage.

If you have to fight a mage without those things, probably the best answer would be to put an arrow in the mage's back. Ideally in a spot right above a vital organ, since if you merely wound a mage you're probably dead. For best results, poison the arrow with something that acts quickly. It doesn't need to immediately kill, it just needs to immediately incapacitate.

If you have to do it in melee, I'd say stab from behind through a vital organ. For best results, poison your blade with something that fits what I wrote above.

If you have to fight a mage who knows you're there, I'd say you're probably going to die. Probably your only chance is to close in however you have to, and then fight as dirty as you can. Throw dirt in their eyes, hit them in the ears, kick them in the sensitive bits, grapple them, just do whatever they look vulnerable to that you think will distract them from unmaking you. Don't keep going with that too long, though: look to have the fight over with as soon as you can, because like Thatsoneevildude said, the mage going abomination is a valid concern. For best results, have a weapon poisoned with whatever you think fits the last sentences of the above paragraphs.

MAYHEEEEEEEEEMMM

that's just a good way to have more people killed in most cases

Only for some members of the Chantry because they don't make a distinction between these two categories.

The best way to defeat mages is by using runes or equipments that have spell resistance ,you put 5 items like that and you are immune to magic,so it doesn't matter what they cast on you they will do 0 damages.