How to change conditions of views filters programmatically?
You specifically ask for altering the View programmatically, and that certainly is possible. I will however suggest an easier way. With Views 3, you can group your filters. This way, you can achieve the effect you are asking for by adding two separate groups of filters.

Group 1: Node:type == [type]

OR

Group 2:  User:role == [role] AND Node:type == [other_type]