The poet has presumably noticed that the spring daffodils, possibly growing in his churchyard, are starting to die off, and he wishes that they would at least stay unshrivelled for the hours of daylight. He then associates them with evensong and prayer, expressing the hope that the congregation will be able to see the flowers still in bloom as they leave church.
There is an interesting hint, worthy of a “metaphysical” poet, that the daffodils, as they droop, are engaged in prayer alongside the parishioners. This depends on the ambiguity of “prayed together”, which could be taken as meaning just the church congregation or including the daffodils as well.