Let's tackle the question of the marigold/aphid relationship first, While some sources say yes, marigolds repel aphids, it would appear that there is no  documented study that says this is an effective way to keep plants from having aphid problems. Marigold roots can indeed repel soil nematodes; but ; it is questionable that the leaves will protect against aphids.
 Dr. Karen Oberhauser, a University of Minnesota  professor in the department of ecology, etc. is considered an expert on the subject of dealing with aphids on milkweed. Her advice is to keep the aphid colony from enlarging (each female can lay up to 80 eggs producing nymphs in a 2 1/2 week period). The best ways to do this are 1) use a spray of water strong enough to knock the aphids off the plant and 2) use your thumb and fore- finger of a gloved hand  to crush the aphids, stem by stem. (You can wash the leaves off after doing this as well.) This may seem unpleasant, but it is effective if you act as soon as you see aphids gathering on the plant. Other techniques, such as spraying with neem oil or  isopropyl (rubbing) alcohol, or introducing predatory lady-bugs, wasps,or surphid flies, will kill the aphids but also harm any monarch eggs or caterpillars already on the plant. Dr. Oberhauser notes: "There is no really good way to kill aphids without killing everything else, except trying to lower the population by carefully killing them by hand."  A few surviving aphids will not deter the butterflies nor harm the plants; a mob scene of aphids will eventually kill the stems and leaves, making it unattractive to monarchs as an egg-laying spot. Your concern for the butterflies is admirable and we hope that you will take the necessary action to welcome them to healthy milkweeds.