Are there any infinite logics that permit infinite, non-well-founded proofs in a controlled way?
SEP's article on infinitary logic has a nice definition of the family of infinitary logics. There are logics like $\mathcal{L}_{\kappa,\lambda}$. $\kappa$ and $\lambda$ are cardinals constrained to satisfy $\lambda \le \kappa$.
Let's assume for the moment that free and bound variables are disjoint sets.
A quantifier must introduce a set of bound variables strictly smaller than $\lambda$. (I think we could equivalently just impose the condition that the set of bound variables is strictly smaller than $\lambda$ because the is-a-proper-subexpression-of relation is still well-founded in $\mathcal{L}_{\kappa,\lambda}$).
$\kappa$ is strictly greater than the size of the largest set of variables that we can join together in an infinitary conjunction $\bigwedge \Phi$.
In section 2, they list an infinite inference rule for conjunction.
$$ \frac{\varphi_1, \varphi_2 \cdots}{\bigwedge \Phi} \;\; \text{is infinite conjunction introduction in $\mathcal{L}_{\omega_1, \omega}$} $$
This results in an infinite proof. In an instance of this inference rule, there are infinitely many open assumptions.
However, a proof containing this rule can still be "unfolded" in a graph that's a tree with a directed edge going from premises to conclusions ... that's still well-founded. (The graph isn't a hypergraph so it loses information about the struture of the proof).
Equivalently, if we start at the conclusion of a proof and work our way backwards picking premises to jump to, we'll always reach the end after a finite number of jumps ... because there aren't any infinite paths through the proof.