It's true that the narrator is not 100% positive about the lovers/patients in the garden. He asks St. Francis to forgive them—which implies they have done something that needs forgiving—and later speaks of "love's first folly". But I don't think he's that negative either. He also speaks of the lovers "liv[ing] / by the Holy light of love / that rules, / blocking despair, / over this garden". I'm not 100% certain whether this "holy" love is the same love that the lovers are exchanging with each other, or if it's a different kind of love that's emanating from St. Francis, but either way it doesn't sound like they're being punished for bad morals.
Also, it would be odd to frame poverty as some kind of deserved punishment in a poem that so heavily features St. Francis of Assisi. Francis was born rich, but renounced his inheritance and adopted a life of extreme poverty in order to honor God and better love others, especially other poor people.
I suspect, instead, that the poet is trying to point out certain parallels between being poor and falling in love.
When you are very poor—a beggar—you essentially have no control over your life. You are dependent on the mercy of others just to live for another day. It is the opposite of being self-sufficient or self-reliant.
Falling in love can be like that. You lose control of your life, a little bit. Your happiness is dependent on the mercy of your beloved; the wrong word from them could wreck you. And you're certainly not self-sufficient.