The noun support takes complements with for, designating what is supported.
I was pretty sure of his support for me.
But the verb support is transitive: what is supported is designated by an object:
I was pretty sure he would support me.
I was pretty sure he would support changing the structure.
An in preposition phrase in this context is a complement: its oblique (the object of the preposition) is 'selected' by support to designate an activity which (it is implied) is performed by both the subject and the object.
He supports me in changing the structure = Both he and I both act to change the structure
A slightly different use, in which the activity itself is the object of support, does not imply participation by the subject:
He supports changing the structure = He encourages the idea or project of changing the structure
He supports my changing the structure = He encourages my effort to change the structure
The for PP in your version is not a complement—for is not 'selected' by support to express a specific semantic relationship. For will be understood here to express the reason why he supports me:
He supports me for changing the structure.
This might be appropriate if (just for instance) I were a candidate to be the organisation's next CEO: he supports me because I succeeded in changing the structure.