If the Swiss declared war on England I doubt that someone in that war would constantly (or significantly casually) bring up the IRA.
There are other Monotheist religions mentioned in the show when Baltar's cult move for equal protection.
Zarek's terrorist past is more prominently mentioned because it is pertinent to the plot at that time.
Baltar's cult is a largely objected to because of Baltar and because of it's links to the Cylons.
The STO were religious terrorists and their links to the Cylons may not be known.