If it hurts, it's probably doing some damage to your hearing. It seems to be an occupational hazard, although perhaps less so for the solo or small group player than for one who sits in the middle of a concert orchestra. (Anyone who sits immediately in front of the percussion section eventially becomes deaf(?))

For practice, you should be able to find a "practice mute" that's a really heavy, usually hard rubber, lump that slips on the bridge and straddles the strings. The usual use is to avoid irritating the "rest of the family" but one of these will really tame the volume while still giving pretty good intonation. A heavy mute of this sort may cut some of the higher harmonics, which can even be helpful while you're trying to learn to get the basic pitch control right.

You will, of course, need to do some practice at normal volume, but note there that a single long exposure to loud noise can do a lot more damage to hearing than shorter exposures of the same cumulative duration, so try to keep the painful sessions in shorter segments and rest the ear for a while before going back.

And if you need them to be comfortable with the sound, don't be afraid to use an earplug. Sevaral kinds are available, and some are intended to block only "impulse" noise (as for shooters) while others reduce high/low frequencies or block all. Comfortable fit is also a problem for some.

If you lack a sufficiently "meaty" jawbone, you may also be getting significant "bone conduction" that sometimes is more objectionable than the airborne sound. A thin softer pad on the chin rest, even just a "hankie" draped over, may help, although you'll have to be careful that it doesn't interfere with a proper "grip" on the fiddle.

John