well, the MLA had no qualms whatsoever with “sacrificing” people like Toga —someone who’s just trying to express her quirks freely, something which is perfectly in line with their goals— to advance their agenda, so I don’t really see why they would have a problem with using the quirk-erasing bullets.
Moreover, unlike Overhaul whose goal is to eventually get rid of quirks, Shiggy just wants to destroy the current system, not erase quirks completely. He’s more likely to use the bullets just to incapacitate heroes.
They also don’t have the means to mass-produce the bullets since it was made by modifying Eri’s quirk factor. Unless the Doc gets hold of Eri and obtains Overhaul’s method of modifying her quirk factor, I don’t see the bullets becoming more than a last resort weapon.
I think theoretically it’s possible for the Doc to “copy” Eri’s quirk into a Nomu (just like what he did with Johnny and the black goo teleport quirk— although it should be noted that we don’t really know whether “copying” quirk is really possible or there's another explanation as of why we saw Johhny using the quirk AFO used), so they have a near infinite supply of Eri’s quirk factor. But then again, the PLF already has Shiggy, Redestro, Twice, Dabi, Geten, and Gigantomachia, in addition to the civilian fighters of MLA. On top of that, the situation with Endy’s family issue and Hawks’ double agent issue— which are just waiting to implode on themselves. The PLF doesn’t really need to go through the trouble of kidnapping Eri, finding a way to obtain an almost infinite supply of her blood, and then obtaining Overhaul’s methods, just so they have more weapons. They already have plenty of weapons to take down the hero society and then some.