The cathedral is one of Poland's most important churches. John Paul II, a Polish-born pope, said his first mass there early in his career in 1947.
Kazimierz Sowa, a prominent Catholic priest and journalist, said: "The Wielgus case made clear there is no escape from the past. We are already seeing that with father Bielanski."
Poland's church supported the pro-democracy movement, which drew inspiration from John Paul II and toppled the communist government in 1989.
Wielgus resigned at the request of Pope Benedict who appointed him only a month ago, and church leaders.
Cardinal Giovanni Battista Re said the pope, who had defended Wielgus as more and more accusations surfaced, did not know that Wielgus had spied for communist police when he nominated him.
Poland is still learning about the extent of the communist secret service's web of informants 18 years after the regime collapsed.
"We mustn't be afraid, and up to now the church in Poland was a little afraid of this issue"
Tadeusz Goclowski, Polish bishop
The country's ruling twins, Lech Kaczynski, Poland's president, and his brother Jaroslaw, the prime minister, came to power last year promising to root out those in public life with close ties to the former communist apparatus.
Some say their drive has also created pressure on the church, which had until recent years been above suspicion, to investigate the archives and name clergy who were informants.
Some churchmen say the time is ripe to face up to the past.
Tadeusz Goclowski, a Polish bishop, said: "I'm convinced that the case of bishop Wielgus will have a cleansing effect and may even speed up certain processes [of change]."
"We mustn't be afraid, and up to now the church in Poland was a little afraid of this issue."