@floodtalonEndian certainly remembers that (Or at least knows about Eos's awesome powers wiping out
someone from existance, if not Artoria specifically), however she'd also recommend that Henry join a stronger side in that case. Lucille hasn't exactly been doing anything on behalf of her minions, and Helena is about as honest as a gun in your face. Plus Henry probably wouldn't be a Machina slave per say, not unless he wants to dedicate himself fully to the Machina. Even Endian knows he wouldn't want to do that. However she'd make a more negotiable compromise so that even if he has to get tacted on with various restrictions and such, she'd find a way around them in order to make Henry more effective at what he needs to do.
Plus there's a pragmatic reason why Endian isn't simply going to start her own revolution; one warrior isn't going to do much against the sheer numbers and forces of the Big Three. By working alongside the Machina, she'd still have access to their resources and power even if her interests may not always aligned with the Machina (Though still in the Machina's greater interest). Mind you, it also relies on the notion that Henry actually does want to make peace with the Machina, Heaven, and Hell, and not simply conquered them himself.