From Burial Box of St. James Found? By James Akin, a well known Catholic apologist:
Some non-Catholics were quick to tout the box as evidence against the perpetual virginity of Mary, however this does not follow. The ossuary identifies its James as the son of Joseph and the brother of Jesus, it does not identify him as the son-much less the biological son-of Mary. The only point that Catholic doctrine has established regarding the "brethren of the Lord" is that they are not biological children of Mary.
What relationship they did have with her is a matter of speculation. They may have been Jesus' adoptive brothers, stepbrothers through Joseph, or-according to one popular theory-cousins. As has often been pointed out, Aramaic had no word for "cousin," and so the word for brother was used in its place. This inscription is in Aramaic, and so there would be little surprise if it were being used in that way.
While the inscription does not establish the brethren of the Lord as biological children of Mary, it does have an impact on which theory may best explain the relationship of the brethren to Jesus. If James "the brother of the Lord" were Jesus' cousin then it would be unlikely for him also to have a father named Joseph. This would diminish the probability of the cousin theory in favor of the idea that this James was a stepbrother or an adoptive brother of Jesus.
The stepbrother hypothesis is, in fact, the earliest one on record. It is endorsed by a document known as the Protoevangelium of James, which dates to the year 120, within sixty years of James' death (James died in A.D. 62). According to the Protoevangelium, Joseph was an elderly widower at the time he was betrothed to Mary. He already had a family and thus was willing to become the guardian of a virgin consecrated to God. The stepbrother hypothesis was the most common explanation of the brethren of the Lord until St. Jerome popularized the cousin hypothesis just before the year 400.
The stepbrother hypothesis is also supported by the fact that Joseph apparently was significantly older than Mary, as he appears to have died before our Lord's public ministry began.
Bottom line: If the ossuary of James bar-Joseph is that of James the brother of the Lord, it sheds light on which of the theories Catholics are permitted to hold is most likely the correct one, but it poses does nothing to refute Catholic doctrine. If authentic, as seems probable, it is to be welcomed as further archaeological confirmation of the life of our Lord.