If someone who had this legacy were to call altruism on an ally, would it lower the duration of whatever maledictions were acquired?

Nope. Unless you get lucky and Altruism purges the malediction entirely, what you take is what you get. This is true even if (for example) you're taking an affect you would otherwise be immune to.

Seems like if I choose a build of warrior that is altruistic and take riddle training to make myself more ready and able to take the hurt of others it'd be a niche build worth making an exception for? The way the legacy is set up seems like it'd be perfect design for this build, based on the helpfile.

It would be relatively a lot of work to get it to work correctly so honestly I'm not likely to do it.