It is safe to assume that they can.
Rules approach
First, let's look at the relevant rules.
Full description of the Holy modifier (emphasis on the relevant part):
A holy weapon is imbued with holy power. This power makes the weapon good-aligned and thus bypasses the corresponding damage reduction. It deals an extra 2d6 points of damage against all creatures of evil alignment. It bestows one permanent negative level on any evil creature attempting to wield it. The negative level remains as long as the weapon is in hand and disappears when the weapon is no longer wielded. This negative level cannot be overcome in any way (including by restoration spells) while the weapon is wielded.
Full description of Beyond Morality (emphasis on the relevant part):
You have no alignment. You can become a member of any class, even one with an alignment requirement, and can never lose your membership because of a change in alignment. If you violate the code of ethics of any of your classes, you might still lose access to certain features of such classes, subject to GM discretion. Attempts to detect your alignment don’t return any results. If a class restricts you from casting spells with an alignment descriptor, you can cast such spells without restrictions or repercussions. If you’re the target of a spell or effect that is based on alignment, you’re treated as the most favorable alignment when determining the spell’s effect on you. Any effects that alter alignment have no effect on you. If you lose this effect, you revert to your previous alignment.
Full description of the Evil subtype descriptor (emphasis on the relevant part):
This subtype is usually applied to Outsiders native to the evil-aligned Outer Planes. Evil Outsiders are also called fiends. Most creatures that have this subtype also have evil alignments; however, if their alignments change, they still retain the subtype. Any effect that depends on alignment affects a creature with this subtype as if the creature has an evil alignment, no matter what its alignment actually is. The creature also suffers effects according to its actual alignment. A creature with the evil subtype overcomes damage reduction as if its natural weapons and any weapons it wields are evil-aligned.
As per Beyond Morality, this Devil isn't Evil anymore but keeps the "evil" subtype descriptor. This descriptor states that this creature ought to be considered as evil for the purpose of effects affecting them.
But then, Beyond Morality also states that, when targeted by an effect based on alignment, that creature is treated as the most favorable alignment. One could nitpick about what "target" exactly means here, but at least to me it seems fair to assume it would cover this case. In this situation, the most favorable alignment regarding the effect the Holy weapon has on its bearer is "any non-evil" and thus that is what would apply here.
Narrative approach
Beyond morality is supposed, thematically, to be a way to transcend your alignment. As a mythic feature, it makes sense that it overrides other rules and is not stopped just by a technicality.
It doesn't make much sense to be both 'beyond morality' toward the whole universe but still specifically affected by one property of a weapon.
