The founder is really suspicious. I think this is one of those choices where you will end up getting fucked several updates in the future. Similar to Annie's pendant of Destiny choice except this is potentially worse.
I have found it difficult to always pick the best choices without using the walkthrough but I was certain this was a bad one for a couple of reasons.
1. Calypso said immortals are bad and if a waifu really has a problem with something, you just dont do the thing in these kind of games. The word immortal was mentioned several times in this scene and raised red flags.
2. Orion has a history with the founder. You can see this when you pick orion's memories in hogwarts instead of penny. So the way the founder spoke to him was a bit off. Although I think that this detail in particular is easy to miss. Its a 1 second clip and it is obvious during that scene that choosing penny over the MC is the correct choice.
3. Probably the most obvious one there is an audio hint that warns you about him at the start of this scene. A clip plays telling the MC to not trust the founder. But if you play without music/audio you will miss this. As a side note if you are playing muted do yourself a favor and turn audio back on. Playing with audio makes the gameplay experience a lot better.