I don't care much about terminology as such, but in the context of OP's example there are two possible interpretations - which you might find it helpful to distinguish between by calling them "true verb" and "gerund" usages. It might also help to consider things using a slightly different sentence...
The Prime Minister promised to stop hunting foxes.
If we understand hunting there as a verb usage (syntactically, the most likely situation), the implied subject of the verb is the PM (i.e. - he promised that he will no longer engage in hunting himself).
If we understand it as a gerund usage, it refers to fox-hunting as an activity (by implication, carried out by other unspecified people), which is semantically the most likely intended meaning. The PM promised that he will stop/prevent other people (everyone) from indulging in the practice (i.e. - he will ban fox-hunting).
In OP's exact context, it's really a matter of opinion which interpretation to apply. Probably the advice isn't specifically addressed to the relatively small number of people who actually do hunt endangered species (it's highly unlikely the writer includes himself in that group, which would be implied by the use of we).
The most natural interpretation is that the writer is using we to mean humankind in general, and that he's advising "us" collectively to stop / cease / abstain / refrain from hunting (i.e. - each of us should voluntarily change our behaviour if we we are hunters).
The "contrived" interpretation is that we're being urged to act collectively to bring an end to such hunting (by voting in politicians who will introduce laws to ban the practice, perhaps).
2The sentence is fine. "Stop hunting endangered species" is a clause within which is the embedded clause "hunting endangered species" as complement of "stop" with "endangered species" as object. In other words, it's a clause within a clause. The verb "stop" freely takes participial ing clauses as complement. (cf. "please stop eating in class") – BillJ – 2016-12-29T10:10:13.533
@BillJ The complement(Hunting..), is it a gerund or active participle? – user178049 – 2016-12-29T10:54:22.097
2Some people would call it a gerund. But many people no longer distinguish gerund and present participle, and would simply call it a gerund-participle. So "hunting endangered species" is a gerund-participial clause as complement to the verb "stop". – BillJ – 2016-12-29T10:58:18.620
The clause "hunting endangered species" is called a catenative complement clause. – BillJ – 2016-12-29T16:56:29.953
Did you mean"endangered spices" or "endangered species"? – Jasper – 2017-03-26T02:08:30.243