How to correctly assimilate dots, if at all?

There is a difference in practice between British and American English. As Larry Trask says, ‘British usage favours omitting the full stop in abbreviations which include the first and last letters of a single word, such as Mr, Mrs, Ms, Dr and St; American usage prefers Mr., Mrs., Ms., Dr. and St., with full stops.’ Etc. does not include its last letter and so the full stop is normally used in both varieties of the language, even when it is followed by a comma. However, when an abbreviation such as etc. comes at the end of a sentence only one full stop is required. On Latin abbreviations in general, Trask's advice is stark, but admirable: 'The rule about using these Latin abbreviations is very simple: don't use them.'

Some abbreviations are so well known that they are no longer normally indicated by full stops at all. They include BBC, CIA, USA, UK, NATO, UN.

I believe that your sentence construct is wrong. You shouldn't put a comma after etc. in the example sentence you've given.

A lion, giraffe, crocodile and bear went to the jungle.

There is no comma after bear.

Etc is short for et cetera or "and other things" in english. Substitute it into your sentence:

There are many examples like mining, farming, foresting and other things that are dangerous to society because they cause environmental damage.

So this won't be an issue as there is supposed to be no comma where you have it in your sentence.

To answer your question, however - in British english it is OK to have punctuation adjacent in a sentence in this instance. The full stop indicates an abbreviation of the phrase et cetera and the comma indicates a clause break, or a pause.

On another note etc doesn't need to be followed by a full stop at all. This might be colloquial, but the full stop tends to be omitted.

If in doubt then you can just substitute in the full word. So for instance this sentence seems awkward:

Its ok Mr., you can stay here.

So, I would substitute in the full word:

Its ok mister, you can stay here.

But that's just preference.