This is a double edged sword. Itachi has no choice. If he sided with Uchiha, the Uchiha will be destroyed by the Village. (Remember the Konoha has many other powerful tribes like Nara, Hguuya, etc...) And contrary to many think, not all Uchiha are created equal. Only a handful of them have the MS and can use Amaratsu, Susano etc. There is no other indication that other Uchiha has that aside from Itachi and Shisui. Say how somehow they survive the Village, they be in weaken state and other powerful village will take advantage of the situation and can take over. In the end the result will be the same, the Uchiha will be left without a village to live and rule and live day by day in the war.
Itachi sided with the Village and spare his brother life. At least his brother will be saved from the misery of the war and many inocents life will be saved. And the Uchiha will have its honor. You also have to look at the anime from Asian perspective. In Asian culture, family honor means everything.
In the end this come down to your morale. Just because they are your family doesn't mean what they going to do is 'Right'. You cannot turn a blind eyes on a possible massacre of many peoples. Say If you know ur family is plotting to bomb a school and kill many kids, are u just going to sit there and do nothing??? Even if you turn ur family to police, you will still feel guilty about not siding with ur family. This is what Itachi feel and decided to live with the decision. Rember his Dad said to him, 'Our pain will only last a moment, while your pain will last forever'. He took the path of a lesser evil. I doubt not many will be able to do that.
