Your batch is not ruined and will probably come out just fine. RDWHAHB.
Boiling the orange peels longer will likely increase the bitterness somewhat, but I wouldn't worry about it too much. Most people use dehyrdated sweet or bitter orange peels from the homebrew shop, which are different than fresh orange peels. When using fresh peels, most brewers try to avoid the white pith of the fruit on the peels as the pith is said to add more bitterness than the peel itself. Also, I am not sure how the peel itslf will cause the beer to become sour, that doesn't seem right. Either way, don't worry, your batch is not ruined.