The mere fact that IDF members are religious or not is not important, discipline is. If these soldiers carry out their orders without hesitation or allowing their personal feelings to overrule their duty, there will be no problem. In fact, their background and understanding may well assist them in certain situations involving the settlers. The real issue is if the IDF is unable to function effectively as mutiny breaks out and military discipline breaks down.
US rally shows support for ex-Marine held by Iran on spying charges (AP)
from the article: Has the IDF become an army of settlers?