Second version has to be with BE: We're not gonna make it.

instead of writing "has to BE"- make it clear and explane why?

1.GONNA is a conversational form of GOING TO, and because COING TO is used with the verb BE, so the form GONNA has to be used with BE: BE GOING TO = BE GONNA . You can't use WILL with GONNA. So, your sentence transforms into : We're(We are) not gonna make it.
2.Actually, since GONNA is a part of a conversational language, most of the people don't even use the verb BE before GONNA. So, they say WE_NOT GONNA MAKE IT. You can say it, but in writing it is considered a mistake. And, the use of the world GONNA in writing is also considered a mistake!
3. Don't use GONNA in writing, use BE GOING TO.