II Maccabees 12 is a big Roman Catholic proof-text for purgatory. The Catechism of the Catholic Church defines purgatory as follows:
"All who die in God's grace and friendship, but still imperfectly purified, are indeed assured of their eternal salvation; but after death they undergo purification, so as to achieve the holiness necessary to enter the joy of heaven" (1030).
1032 states, "This teaching is based on the practice of prayer for the dead, already mentioned in Sacred Scripture: 'Therefore [Judas Maccabeus] made atonement for the dead, that they might be delivered from their sin." The quote is from II Maccabees 12:46, showing the book is important for Catholic doctrine.
The problem is this: Roman Catholicism asserts that purgatory is for believers who have committed "lesser faults." What was the fault of the soldiers for whom Judah the Maccabee was praying? In II Maccabees 12:40, we read: "Then under the tunic of each one of the dead they found sacred tokens of the idols of Jamnia, which the law forbids the Jews to wear. And it became clear to all that this was the reason these men had fallen" (NRSV). Their fault was idolatry.
But Roman Catholicism doesn't deem idolatry to be a "lesser fault." It takes seriously such verses as I Corinthians 6:9-10 and Galatians 5:20-21, which categorically declare that idolaters will not inherit the kingdom of God. The Catholic Encyclopedia states that idolatry--and even the simulation of idolatry to escape persecution--are serious mortal sins (see here). And people aren't cleansed of mortal sin in purgatory (see Thomas Aquinas' words here).
How do Catholics reconcile this? I'm not sure how the church officially does so, but I found the following answers on Purgatory and 2 Maccabees - Catholic Answers Forums:
"IT is an example of praying and offering a sacrifice for those who have died, for God's Mercy. No individual ever knows the fate of another individual. There was simply hope."
"We can debate whether or not the sinful soldiers were actually aided by this sacrifice or not, in light of the severity of this sin. However, what is not up for debate is that Judas thought it wise to offer such a sacrifice for these dead soldiers, in the hopes that this sacrifice for the dead would help them in transition from this life into heaven (Judas undeniabl[y] believed in purgatory.) And that his belief here is scripturally commended as 'holy and pious.'"
"There is nothing in this passage that indicates that these men were guilty of mortal sin. The wearing of amulets in itself is not necessarily an indication that these men were engaging in full-blown idolatry -- they could have been guilty of something as simple of simple superstition or 'hedging their bets' by wearing these amulets as good luck charms. Judas and his men, in any case, are (after the fact) in no position to know the mindset of these men. All they know is that these men are guilty of at least superstition and offered prayer and sacrifice for this purpose. These men did not presume the dead soldiers were guilty of mortal sin, just as we Christians should not, who pray for the repose of the souls of our loved ones."
The last explanation is probably the best. According to What is a Mortal Sin? on the Catholic site, www.saintaquinas.com, mortal sins are deliberate. Or, as the Catechism states in 1859, "Mortal sin requires full knowledge and complete consent." Were the soldiers in II Maccabees 12 deliberately worshipping idols with the full knowledge that there is only one God, meaning that idols are useless? Maybe. Maybe not. You'd expect them to know better, since they lived in a Jewish culture that recognized the one true God and the uselessness of idols. But perhaps they thought that God wasn't enough to protect them in battle, so they resorted to idolatry. They were ignorant in that they didn't know God's full power.
But if ignorance is an excuse, doesn't that release most idolaters of guilt? Most people who worship idols sincerely believe in their efficacy. Otherwise, why would they do it?
Also, the Bible is mixed about whether idolatry is a sin of ignorance, or one committed in full knowledge of who God is. Speaking about idolatry, Paul affirms in Acts 17:30 that "God has overlooked the times of human ignorance." Yet, in Romans 1:20-23, Paul says that the Gentiles knew God because they could see his power and deity through nature, but they chose not to acknowledge him, which led them into idolatry.
But II Maccabees 12:45 says that Judah offered the sin offering for the dead Jewish idolaters because "he was looking to the splendid reward that is laid up for those who fall asleep in godliness." Does that imply that they died in a state of godliness? Maybe they weren't completely bad--only imperfect, in that they clung to good luck charms in a vain attempt to keep themselves alive. But at least they were willing to fight for God and his laws, and that says a lot.