All shuls should absolutely should make a mishebairach for the chayalim.
Even my AGUDAH does it! Of course they don’t, chalila, use the form that mentions the state of Israel, but a nusach was created and it is said every Shabbas.
Those who believe you are protected by the Torah learning ALONE going on there (and I do not at all deny the extreme value of that learning) must feel that Israel, even the way things are now, merits such a naiys niglah without the hishtadlus of the IDF.
Those of you who oppose such a tefila, NEVER, I hope, step foot in Eretz Yisrael, because it IS the presence and the actions of the chayalim that keep you from getting your throat slit!
Furthermore, even before your plane lands at BenGurion airport, you are making use of “the Zionist infrastructure” – from the control tower at the airport, to the use of the Zionist cell phone system you use (to call your learning son, or son-in-law, to tell them you’ve arrived), to driving on the Zionist built roads, to arriving at your Zionist built hotel, and washing your hands from a Zionist built water supply system, to plugging in your shaver, or your phone charger to the Zionist built electricity supply, etc., etc., etc. One would have to be an extreme hypocrite to be so anti-Zionist and still make use of all they have done!
I personally am as strenuously against and disgusted by MANY of the policies of the Israeli government as any person could possibly be, but the way to make a HUGE kidush HaSh-m and change the face of Israel into be a Torah state is for a hundred thousand (or more!) frum Jews to make aliyah, NOT by sitting in the U.S. and thinking you are holy by not praying for Jewish boys, religious and not (yet) religious, who are putting their very lives on the line to protect the Jews in Eretz Yisrael INCLUDING the ones who are anti-Zionist, INCLUDING the boys that sit and learn, and INCLUDING YOU when you make vacation visits!