Hi Vanessa,
I think it is pretty common for babies to get a little constipated from formula. Offering the cooled boiled water is something I had been doing since the beginning... I wouldnt worry too much about becoming reliant upon, I guess we just need to do what works.
Aidyns constipation was on and off for many months, and when he was over 4 months I was able to help things along by giving him pureed pear... that works wonders!
But yeah, it is pretty distressing seeing them in pain when trying to poo. I suggest just sticking to what the Dr/chemist told you - I seriously doubt that you would be doing any harm by it.
I hope things settle soon... from memory it does get better after a month or so, but never completely dissappears.