How do I remove the quarantine?
I'm not sure what you are asking here. The quarantine is a metadata flag. You can remove it with xattr, but that is unlikely to help. You can's ship with that.
How do I get the system to put those process in the same sandbox the parent is using?
Again, you have to be careful with your terminology. I'm pretty sure you are asking about the app's container folder here, not the actual sandbox, which is a runtime environment. Obviously you could just copy files into the sandbox, but again, that's not going to be helpful. When your process spawns another process, by default, it inherits the same runtime sandbox. That isn't helpful to you either. You are asking about a system restriction which you can't change.
I'm not running it from the bundle cause it fails from there as well, probably for the same reasons.
What is this "probably"? There is no "probably" in software development. Either you know the cause, or you don't. Speculations and assumptions are only useful when you have several days where you really need to be frustrated and unproductive.
I suggest you stop here and investigate this failure. Then you will be able to run from the bundle and keep your complications separate.
More importantly, assume I want to download plugins from the internet, from my curated website, with helpers, and deploy them to ${sandbox}/Library/Plugins/. From what you're saying I wouldn't be able to run these?
Well that's a can-o-worms. What's the big picture here? Why are you sandboxing? Is this for Mac App Store deployment? Before you spend too much time on this idea, you have to make sure your app idea will pass App Review. App Review does have a category for "plugins" but it is up to you to interpret it and ensure that your app will comply. Apple won't "preclear" apps for App Review. I strongly advise making the "plugin" idea an optional afterthought that you can disable, if necessary, and still have a viable product.
If you aren't deploying via the Mac App Store, then you have more options. In no case is hacking inside your app container a really good idea. You'll have to be careful with this and structure the UI such that users can drag their plugs into the folder. Your app can conveniently open the container folder for them in the Finder, but the sandbox will cause problems due the the restriction that eskimo mentioned. But if you aren't deploying in the Mac App Store, do you really need sandboxing?
There are a number of ways, sandboxed or not, to make binary plugins "available" to your app, depending on your implementation.