Symbolism, Imagery, Allegory
Isis is a pagan god originally from ancient Egyptian mythology, so the presence of her temple in the middle of a Christian, English poem might seem odd. What might seem even more odd is that the Temple of Isis appears to be a kind of stand-in for a Church and it is a place that does not embody the threat of heathen belief, but rather offers solace and spiritual clarity to Britomart.
In this sense, we can understand the Temple of Isis as a representation of the origins of Christianity, the practice of spiritual truths before Christianity existed. Isis was a goddess associated with both marriage and childbirth, so she's an appropriate vehicle for Britomart's vision of her own future marriage and line of descendants.