I do not see how it really weakens them even when raised indoors out of the elements as long as the rearing containers are properly cleaned and disinfected to prevent the spread of disease.
I raise all of my monarchs indoors. I do NOT raise them on potted plants or anything like that. Every day or so I collect leaves from outdoors to feed to them (any left over leaves I put in the fridge for the next day's feeding). I have about 200 insect rearing cups with special ventilated lids that provide good traction for the cats. I prep a clean cup and line it with a square of paper towel and fill it with milkweed leaves and move cats from their dirty cup to the new cup. The dirty cups/lids are soaked for 30 minutes in a strong bleach solution and then washed with soap/water and air dried and are then ready to be used the next day. The milkweed leaves are scrubbed under cold running water and then towel dried before being fed to the caterpillars. I do NOT use bleach or anything else to clean the leaves.
I have also begun keeping my cats sorted together based on where they were collected. I used to keep them sorted by size regardless of where they were collected, but the incident of illnesses was much higher. Since I stopped mixing groups in with each other the number of illness related problems dropped drastically. And I also work to clean and feed cats from one collection site at a time and wash up before moving on to the next group to help prevent any possible cross-contamination. Also, if a particular group is exhibiting illness, I always try to do them last and start with the healthiest looking groups first.
Most of the 5th instars are moved to custom built metal screen cages (a different cage for each collection site) a day or two before they go into their chrysalis. The insect rearing cups are plenty large to allow 5th instars to make their chrysalis if necessary (can handle up to 4 chrysalis without problem). Sometimes I misjudge and they make a chrysalis before I have time to transfer to a screen cage. Any cats that exhibit illness or look "off" are kept solitary confined to the insect rearing cups to make their chrysalis there.
If I am out collecting wild cats and I find 4th/5th instars I usually like to keep them confined to the rearing cups to make their chyrsalis in case they are harboring fly parasites..this way I don't have to disturb existing chrysalis in a cage setup by trying to pull out the dead hanging cats or failed chrysalis.
If anything I think it helps to raise and release the adults in areas where milkweed now exists but didn't before. I think there is some inherited GPS tracking gene in the butterflies that they pass on to their children.
My house... took me years to get a good milkweed patch going... but once it was going I never got any monarchs visiting/laying eggs. Then a few years ago I started actively releasing adults I raised from cats that were collected elsewhere. Since I started releasing adults at the home garden, every year since I get a few monarchs visiting. And I am seeing larger and larger numbers of eggs being laid on my milkweed. Last year I collected well over a hundred eggs. This year looks to be a bumper crop again.
Same thing is happening at work... We built a new garden and planted lots of milkweed. Nothing the following season. Released adults that summer that had been collected from elsewhere. The next year.. we had monarchs visiting that were laying modest numbers of egg. Grew them cats up and released them. Last year our population exploded. This year the population is still quite high.
Last year I collected every egg/cat I could find to raise (collected over 700, tagged 550). It was a lot of work. This year because I am seeing such a strong turn out for egg laying again, I decided to just let nature take its course on the eggs. I don't have as much time this year so I am only concentrating on collecting and raising cats and babying eggs takes a lot more effort than dealing with already hatched cats. Every 3 days I go looking and collect cats, but leave eggs where they are. The only eggs I am raising this year are those I accidentally collected when pulling leaves to feed to the cats (i try to look for eggs first so I know what leaves to not pull, but sometimes I miss a few). Ants are not too bad this year. Ladybug population is nuts though. Even so with the predation on eggs and tiny cats, I am still collecting plenty of survivors that I will probably be able to tag 300-500 adults this year.
I am a month into my rearing season and already raised and released 46 adults (tagged 41), have 102 currently in chrysalis, have 140 cats (ranging from 1st - 4th instar), and 5 eggs... and it's not even the peak of the season yet.