The scientific community will actually be protecting them not the other way around.
If they are sapient and intelligent that alone will go a long way, provided they have a dialog with humans. Scientists do not act as they are portrayed in movies. Modern science has some really strict ethics about how to treat sapient creatures, and consent laws will almost certainly apply here. Now scientists are going to WANT to investigate and will probably never stop trying to negotiate research deals with said creatures, but modern scientific ethics will keep it strictly voluntary and on the creatures terms. More importantly the scientists will want to go to them in their natural conditions not capture them, they will be just as interested in their culture as their biology.
Just look at modern anthropology minimal interference and maximum consent is tantamount. As an example you can look at the [sentinel island][1]sentinel island peoples who have zero contact with the outside world because they don't want any. The consent of the patients involved is essential. Now this is only going to go so far, if one of them dies on the streets of a city the scientific community will be all over it like flies on a carcass. And if they are trading with humans then there will be scientists constantly asking to study them and their culture, with varying levels of bribery to achieve it.
Part of it is dependent on where they live and how easy it is to get to, if it is very easy to get to you will have poaching. If they are near a dictatorship or country with little respect for individual rights they will be captured. This goes double if they enter such a country. But if they are only reachable through countries that respect individual rights (the majority of countries) they should be fairly well protected. There will be incidents but they will be rare.
Your biggest issue will be military investigation, the military had better be sure they cannot pass for human, or they will consider them a threat, and will investigate.
You should also make first contact very recent, because the ethics of the past was very, VERY different.
You may also want to consider how to keep one of the creatures from volunteering for research given that they will likely be offered millions of dollars for some scans, tissue samples, and demonstrations. [1]: https://en.wikipedia.org/wiki/North_Sentinel_Island