A weapon that is +5 or better is considered all alignments for the purpose of bypassing aligned DR. The rule is in the Glossary section in the rules for Damage Reduction.
Also, the same section says
"Overcoming DR: Damage reduction may be overcome by special materials, magic weapons (any weapon with a +1 or higher enhancement bonus, not counting the enhancement from masterwork quality), certain types of weapons (such as slashing or bludgeoning), and weapons imbued with an alignment."
But the beastiary section on damage reduction also says
"Some monsters are vulnerable to good-, evil-, chaotically, or lawfully aligned weapons. When a cleric casts align weapon, affected weapons might gain one or more of these properties, and certain magic weapons have these properties as well. A creature with an alignment subtype (chaotic, evil, good, or lawful) can overcome this type of damage reduction with its natural weapons and weapons it wields as if the weapons or natural weapons had an alignment (or alignments) that matched the subtype(s) of the creature."
I don't think that an intelligent weapon having an alignment is the same thing as it being imbued with an alignment (such as it would have if it had the Holy ability) and it wouldn't have the alignment subtype automatically anymore then a player character would.
