On what are you basing your premise? Wikipedia gives roughly similar number of "non religious" people in Lithuania (6%, 2011) and "atheist + non believer/agnostics) in Poland (5%, 2013)

Let's make few things clear, while commonwealth was treated like one country, it still was two separate countries inside of it. Certain things were carried from one country to another (f.e. noblemen rights from Poland to Lithuania and certain laws/military organization bits from Lithuania to Poland), but in the end, it was two countries. Lithunian common folk was speaking lithuanian (in was considered the language of poor people, walthy people and people with rank spoke Polish, and just to make things clear, how deep it was, if you were nobleman in Lithuanian during those time, even if you had no mony, only sword, you would still speak Polish, because you were nobleman and not some lowly farmer), celebrating Lithuanian pagan holidays, while Poland was concentrating on Christian holidays. And not to mention, Christianity in Lithuanian started as a part of war strategy

Might have to do with cultural history. Polish history is littered with catholic saints, heroes and kings. Catholicism is intertwined with the personal identify of the Polish people. A lot of other European countries don't have that strong of a connection.