It is true that Jerome did not initially accept 2 Maccabees as Scripture and thus would not have used the texts from the book to support belief in purgatory. But this in no way undermines the canonicity of 2 Maccabees.
First, Catholics do not consider the early Church Fathers as infallible. Therefore, one should expect to find some Fathers teaching things that are not consistent with later defined teachings.
Second, there is evidence that Jerome later accepted the deuterocanonical parts of Daniel despite the belief of the Jews of his day that they were not Scripture. In his response to Rufinus (11:33, A.D. 402), Jerome makes explicit that it is the judgment of the church by which the canon is to be settled. He writes, “What sin have I committed if I followed the judgment of the churches?”
Jerome would also eventually include all the deuterocanonicals in his Vulgate edition of Scripture.
So, rather than Jerome’s initial denial of 2 Maccabees’ canonicity undermining the Church’s acceptance of the deuterocanonicals into the canon, the story that his denial is a part of actually supports it.
For more on this topic, see Jimmy Akin’s article, “Defending the Deuterocanonicals.”