Yes, the official STO installer/patcher/launcher is apparently a stripped down torrent client.
It doesn't have any way of limiting uploading.
This means...you're probably best off trying to get the client some other way.
For instance, you can access the client torrent from Cryptic with a third party BitTorrent client of your choice that does allow you to limit uploading.
That's the torrent linked off the Support -> Download page, by the way. Cryptic doesn't offer any other official downloads, but other file hosting sites may have client downloads as well...possibly of older versions, however, which would mean a considerable amount of patching.