The word "it" refers to their building of the altar. Alternate translation: "If we built this altar in rebellion or breach of faith against Yahweh" or "If we rebelled and broke faith with Yahweh when we built this altar"
"do not rescue us today" or "do not save us today." The three tribes say this to prove to the rest of Israel that they did not build the altar in rebellion or breach of faith. If they had rebelled and broken faith, they would not have dared to say "do not spare us on this day."