Wrong, PIS the political party was founded in 2001 and the word Sanepid had been used long before that.
But maybe this institution got the name "Państwowa Inspekcja Sanitarna" after 2001, the name was different before and explained well the word Sanepid?
PKP - Polskie Koleje Państwowe is a Polish thing so it's obviously pronounced Polish way.
But for example, I often hear the name WORD (Wojewódzki Ośrodek Ruchu Drogowego) pronounced like the English word "word". Which doesn't mean that it's correct, but it's how people speak.
It wouldn't be probably so if "Word" wasn't also a name of a popular computer application :)
To be strict, the Polish pronunciation of the name of the text processor isn't ideally correct in English ("w" is pronounced in English way, but "o" in the Polish manner), and it's also how Polish people often pronounce that abbreviation.