I'm going to ignore that her condemn is 50% bonus AD and another 100% bonus AD. I'm also ignoring that her ultimate means she can stay invisible in fights for eternity. I'm gonna ignore a lot of things.
Legit, in my opinion the best way to make it so that Vayne is a bit more fair while still keeping her a strong champion, is to remove the true damage on her silver bolts and instead have it do magic damage. Not scaling on AP, just magic damage. Keep all the damage as it is, just make it so that it's magic damage instead. This way, if vayne is still ahead, she'll still make you explode, but at the very least, tanks won't instantly blow up in a few solid hits.
No this won't answer the problem that vayne is still a ticking time bomb and any kill you get her on her is only delaying the inevitable. However, at the very least, tanks can actually build against her and won't just be giant meat wads for Vayne to gobble up.