The denotation, the literal meaning, of "temperate" means moderate and not excessive to one degree or another. In other words, the speaker is saying that his beloved is like the baby bear's porridge in the story "Goldilocks and the Three Bears." It is not to hot and not too cold. It is just right.
The speaker elaborates on this idea in the rest of the poem. Sometimes the sun is too hot and sometimes it is too dim. Summer is also too short and the plant life eventually loses its foliage ("untrimm'd"). It's either bursting with life or that life is fading and withering. The summer's day is too erratic, whereas the beauty and character of his beloved are more temperate, more constant, and consistently good. That is to say she is "just right." In one sense, the speaker seems to be saying she's not as miraculously beautiful as a perfect summer's day. But he also shows that the summer day varies and is undependable.
He ends the poem by implying that the poem itself will live on forever. Whereas a summer is fleeting ("too short a date"), her "eternal summer shall not fade." He is making the point that her beauty (spiritual, but perhaps physical as well) is eternal. But it is the poem itself that solidifies that immortality. It will live on "in eternal lines."