Speaking from personal experience, Israel is the only place on earth with a startup ecosystem comparable to the Valley.
tl;dr I think the Israeli army if anything is a massive contribution to the success of their innovation economy.
(1) http://www.amazon.com/Start-up-Nation-Israels-Economic-Mirac...
"Start-Up Nation addresses the trillion dollar question: How is it that Israel -- a country of 7.1 million, only 60 years old, surrounded by enemies, in a constant state of war since its founding, with no natural resources-- produces more start-up companies than large, peaceful, and stable nations like Japan, China, India, Korea, Canada and the UK?"