Make users understand that a deep link is both to download and to use in the application

The main problem with that solution is that it satisfies two very different needs. If it is a simple link, such as "http://foo.bar/joingroup_x", there is not much you can do. Or change the name of the last part of the url to be clear, by clicking on the link that will join a group or install the application (such as "http://foo.bar/install_app_and_join_group") or place a description in somewhere near that link, which should be stylized so that the user notices it.
Another way could be to use a button with a descriptive label.

However, both are not good solutions, but you need to communicate in some way the two different attempts.

I do not know his motivation to implement it that way, but I think he wanted to reduce the effort necessary to join the application. You can consider re-dividing those two functions, since it seems that the built-in installation function is not really necessary and may not fulfill its function.