How can we effect institutional change to make academia climate-compatible?
I can think of two main ways to reach these goals:

Method 1: grassroot campaign

For example it could go something like this;


Create a group of researchers from various fields who share this goal.
This group reaches a consensus for a set of realistic measures that an institution could pledge to apply. 
Reach to the most prominent scientists from various fields, ask them to: 


publicly  support the pledge
lobby the institutions/organizations they belong to to sign it
boycott the conferences which don't sign it.

Keep the pressure from the scientific community until most major institutions are compelled to sign the pledge. At this stage extend the scope of target institutions to funding bodies and big industries.


Rationale for targeting the most prominent scientists: because they have the visibility and influence, they are on the board of the most important conferences, they can afford to boycott conferences and their boycott could destroy these conferences.

Method 2: patience

This kind of measures are going to be taken sooner or later, when the damage is too obvious to be ignored (recent research point to more death caused by air pollution than by smoking). At some point it will simply look ridiculous for academic institutions and funding bodies to insist on ethics in research while paying travel expenses across the globe for researchers. But that's going to take a while.