How to deal with alma mater pushing crack science? I am aware that in US there is controversial support of facilitated communication and every public is dealing with a different kind of process.

The European university and faculty where I finished my BSc are very good and respected.
However, they have begun to push an agenda against an industry project due to environmental concerns. More specifically, the student association opposes the project and tenure-track staff and lecturers from the biology and ecology departments started to support this cause.
All of this is not based on evidence.

How can I stop and intervene in the matter of my alma mater? This is reputation-damaging as it not appropriate for an educational, academic, and research institution to spread such non-sensical ideas.
Do not intervene.  It won't work, and may damage you.

Political and ecological matters can be highly divisive.  No project has zero impact, so even if everybody agrees about the facts, strong disagreements in the balancing of pros and cons are likely to remain.  Therefore, the most likely outcome of trying to intervene is that you make enemies, without being one step closer to your desired outcome.  It is very unlikely that you will be able to convince students and faculty that they should change their opinion or actions on this.