I'm not seeing how converting the spell-like ability to a supernatural ability helps. It still does cold damage, so immune creatures take no damage. It is still not a spell, so you cannot apply the metamagic feat to it.It would be reasonable to ask the GM to allow a Piercing Cold Spell-like Ability feat, modeled off of the other metamagic feats.
The prereq would be caster level 2, and you could only apply it to a SLA whose spell level was at most half your caster level minus one. You could apply the effects of the feat three times per day.
For example, if your SLA duplicates a second level spell, you would need a caster level of at least 6.
If you go down that path, it might make sense for you to also ask about an SLA version of Energy Substitution.
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