Pivovarsky Dum is cool but no bottles. Same folks who own Pivovarsky Klub. If she likes beer she should go and get the sampler. They do cherry and nettle and coffee and other flavored beers. The regular light and dark lager are very good. They have an almond mead that they serve pours of (not made by them) that is awesome but I never made it back to ask if you can buy a bottle to go.
Pivovarsky Klub is a bit of a hike from the city center, but if the weather is nice it isn't a bad walk. We did it in about an hour I think (each way). It is non-smoking which is not common and which I like. Food is outstanding (Bourdain went there on no-reservations).
You can get bottles to go there, I doubt there is a better selection (probably 500-800 total, 100ish Czech). I like Bernard products. I see them sometimes in the US but not the same (stale).
I would have her get you a range of Czech light and dark lagers. They are all pretty characterful, I think. Tell her if anything looks really interesting grab it. Tmave is "dark" and the gravity in plato is usually part of the name of the beer. They also have mead (medovina) in bottles to go if that is your thing. It's okay, and a novelty, but not great. Make sure she only gets you Czech beer, most of the imported beer is the same as we get in the US and not any cheaper.
U Medvidiku has some bottles to go including some stuff that is very idiosyncratic for CR (strong, flavored etc). That is right in the city center.