On Ioannis GM, as things stand, he is the heir presumptive of the Lascarid realm by virtue of his marriage. Alexandros' rushing to see the wedding concluded was very much understandable in this regard. Without his in person sanction, Ioannis place in the line of succession could have been seriously disputed and threatened, which in turn would have made the regency unstable. This gives Agnes a few years of peace, but it all depends on how much loyal Ioannis and Adrienne Jr are.
Then, Agnes won't be alone. Don't forget Grandma Adrienne, the family's matriarch.
She has been around for almost fifty years now. As Theodore I's widow, she is probably the most experienced person of stature in the Lascarid empire, and in the time since Agnes arrived in Syracuse, I'm sure she would have tutored Agnes in the way of Lascarid politics. With Theodore and Alexandros away on campaign, they surely spent a lot of time together.
She is into her seventies, but if she lives as long as, say, Eleanor of Aquitaine, she might be around for ten more years.