I agree with you here. Infusing religion with military or politics is a major concern. How do we decide which sect to promote when there are dozens of people each believing in his or her own version of Islam, there are sects there is shia sunni and much more. The difficulty of imposing religion makes it clear that secularism is a much better concept where religion is a personal thing. I would also like to note that there are differences between scholars of one sect too on several subjects. For example the ruling on beards. Some hanafi scholars say it is necessary while others say it is sunna. So who should we believe and which law should we promote in our theological states, beards or beards voluntary...
As is obvious it shows that a country where religion is infused into our laws cannot function properly.
Zia Ul Haq, when faced with this problem in imposing his version of Islam gave sanction to Sunni view of things alienating the shia which resulted in the formation of groups like Tehreek e Jafaria and Sipah E Muhammed. Iran has also partly done this alienating sunnis in their country.
I think we need to look at the secular model much more positively. Ataturk was seen very positively by Iqbal and Jinnah too was a staunch supporter of secularism.