As long as you keep them seperate and sell them seperate, that's fine. Just make sure the LFS knows which are which.
But the thing is, guppies and endler's, like I've said before, don't produce anything special. You can go out to your LFS and buy an endler's hybrid right now (fancy double-sword guppies). That's why I keep saying it's pointless to bother with the hybridizing when you can produce pure endler's instead which are worth so much more (not necessarily money-wise mind you).
I would, if you're looking to hybridize something, try the molly X guppy cross. I thought I'd managed it successfuly once. I'm no longer so shure. I don't keep mollies any more so I'm not in a position to attempt it again myself. Molly hybrids are harmless to wild populations because they are not going to flood the market or the wild and they certainly can't over-take guppies or mollies, plus look significantly different to either parent species.
See? I'm not fully against hybrids or hybridizing - I'm just against this particular cross. The other I've considered is pearl gourami X three-spot gourami - but I wouldn't pass them on in case a mix-up occured somewhere down the line. I've always wondered what fry from this would look like. It's just the tank space that's keeping me (because I'll need to keep them all...)
Anyway, I'll explain how hybridizing fish in captivity (with endler's in mind) can cause harm to wild populations... You breed the hybrids, you're removing pure endler's from circulation within the hobby. People want pure endler's. They can't get pure endler's. So what to do? They take the endler's from the wild. The other way in which they can cause damage is if some do happen to get released into the wild (think of people who flush

). This danger already exists, however, due to all the hybrid fancy guppies. Still, adding to it can't be good.
Unfortunately, people are not as you described. Humanity has never shown much interest in preserving wildlife. Sure, there are organisations and plenty of caring people who want to keep Siberian tigers or orcas alive - but not many care about your average aquarium fish. The thing is, while you or I are willing to give up a patch of land or some of our homebred fish for the sake of wild populations, we are a minority. People simply don't care. Even if more people did care, the number of pure endler's within captivity may not be enough to provide the (genetic) basis for a new population. That's why it's much better to work at preventing wildlife from becoming endangered rather than looking for solutions later on - when it's likely to be too late. You've only to look at Thylacines (Tasmanian tigers) - the last of which died in 1936 in a zoo - to see that, even quite recently, and even with larger animals, we've let wildlife down and looked towards solving a problem once it was all too late.
I'm going to stop lecturing you

Sorry about *nearly* losing my temper before. I just want people to realise that they
can have a huge impact on wildlife even if what their doing seems to be limmited in it's effects to captivity. Just be aware of what you are doing. Like i said before, your plan to keep the pure endler's seperate from the rest is a good plan. You can sell the rest as guppies (even the hybrids). Just make sure your LFS realises they are different and does not take them all as 'pure' endler's.