I saw an organ accompaniment in phrygian (or hypophrygian) (E as finalis). The last chord was C major. Should we end phrygian and hypoohrygian on a major chord?
The question is what you mean by "Phrygian." Particularly when you introduce terms like "hypophrygian," you are referencing melodic classifications like those used to discuss monophonic chant. Phrygian, in that case, just means that the finalis falls on E. Whether it's just "phrygian" vs. "hypophrygian" is an indicator of ambitus (i.e., range). Often there are characteristic melodic gestures, recitation tones, and cadential patterns for such melodies in those modes too.
If all you're referring to is the mode of the melody a piece is based on, then there are often many possible ways to harmonize the melody. The most traditional method would be to retain an E-based chord (usually minor) at cadences, perhaps with a concluding turn to an E major chord at the final cadence. (Historically, the major chord was viewed as a stronger consonance than the minor triad, so minor mode pieces often would end with a major chord.) But both historically and today, Phrygian chant melodies have been harmonized to end on another chord, such as A major/minor or C major.
Bottom line is that melodic classification of a chant melody is one thing, while the actual chords and key a piece may be harmonized with could be another. Modern pop/jazz theory treats "Phrygian mode" as something that is primarily based on chosen notes of a scale and harmony, but historically words like "Phrygian" and "Hypophrygian" were about melodic features.
So when you say the "organ accompaniment" was "in Phrygian," I'm unsure what that means. Does it mean that the harmony was based in chords drawn from an E Phrygian scale (which would include C major)? Does it mean it was an organ accompaniment of a chant that's in the Phrygian melodic mode? Regardless, the choice of what chords to choose to be in an accompaniment is flexible depending on what your priorities are and what sound you like.
We can actually finish any piece on any chord - there's no ruling to say otherwise!
Minor pieces can and do finish on a major chord; it's from the parallel key, and it's called the tierce de Picardie.
But in your case, it seems like the piece is in E Phrygian, the parent key of which is C major. So throughout the piece, the diatonic notes from C will have been the most used. It won't be too jarring to finish on the root chord from that key. And, it contains an E note anyway.