DY- It doesn’t matter. If you found out that the composition of the tefilah was in fact a genuine prayer to protect those soldiers who fight for us without ulterior motives, would that change your opinion? I doubt it. You oppose it because it practically has Zionist connotations today. It’s not the reason why most people say it. And it may or may not be the reason why it was started. But the connection between a prayer for Israeli soldiers and Zionsim is quite obvious and the reason why most in the Charedi community don’t say it.
Why it was started doesn’t practically matter- those who don’t say it, won’t say it regardless of the motivations of its authors… and those who say it will continue to say it regardless of the motivations of its authors.