Missed this thread originally but just read through it now.
Can't believe how badly the school are treating you 
Although I'm a mum of boys, I absolutely think you're in the right and the school are completely in the wrong on this matter.
In addition to all the other great points that have already been raised, a couple of thoughts spring to mind...
If it's a Roman Catholic school then maybe ask them to show you exactly where in the bible (or indeed in any other papal decree or similar) it says that boys have to wear trousers and girls have to wear skirts.
Have you spoken to your local diocese officials? Do any of the other local RC schools allow girls to wear trousers? If there's one or more that do then they'll have problems arguing that there's any sort of traditional aspect to this.
And maybe point out that given all the problems that RC schools have had in the press in recent years, it seems strange that they are insisting on a uniform option for girls that ensures their underwear is shown whenever they sit cross legged, and regularly when playing in the playground assuming they still do handstands etc like we used to when young.
Ask if they are so concerned about being traditional etc that they are going to make all teachers wear skirts or pinafores and not allow them to wear trousers any more.
Ask them to provide proof of how boys are able to look smart wearing trousers but girls aren't able to look smart wearing the identical trousers (I'm assuming here that you can buy generic [colour] trousers from a local supermarket / m&S / John Lewis / etc and the girls trousers are pretty much identical other than having a pink label on instead of a blue one, same fabric, similar cut etc etc) and maybe say that you're worried about the mothers of boys choosing cheap trousers that will go all shiny so maybe they ought to make the boys wear skirts as they seem to have established that skirts are smart while trousers are not.
Remember that you're not bringing the school into disrepute by bringing this to everybody's attention - the head teacher and the governors are the ones that have done that by voting to refuse to allow trousers for girls.
Do a straw poll in the playground of the parents to see how many agree with you and how many don't. Note to see if there are any differences between parents of just girls, just boys or both boys and girls. See if they have been fobbing you off. Particularly get to the parents in the new reception year as there's a fresh batch of people who will hopefully be more enlightened and want the option of trousers for their dds. Plus they might have more energy to fight onwards if you've been tired by it all - not surprising after the dreadful way the school has been treating you in this matter.
Contact Everyday Sexism - this is just the sort of thing that they are campaigning against - the entrenched ideas of a female's place that puts them at a disadvantage.
www.everydaysexism.com/