There are two adjustments that can be made:
(1) the vertical line separation, and
(2) the horizontal labels space.
% !TeX TS-program = pdflatex
\documentclass[12pt,a4paper]{article}
\usepackage{amsmath}
\usepackage{proof}
\begin{document}
\noindent Original setup \\
\infer[(\implies I)]
{
(q \land r \land ¬s ) \implies ( u \lor r )
}
{
\infer[(\lor I r)]
{
\\u \lor r
}
{
\infer[(\land E_{2} r)]
{
r
}
{
q \land r
}
}
}
\vspace*{50pt}
\noindent Increase the line separation \\
\setlength{\inferLineSkip}{6pt} % increase the lines skip added <<<<<<
\infer[(\implies I)]
{
(q \land r \land ¬s ) \implies ( u \lor r )
}
{
\infer[(\lor I r)]
{
\\u \lor r
}
{
\infer[(\land E_{2} r)]
{
r
}
{
q \land r
}
}
}
\vspace*{50pt}
\noindent And also increase the labels separation \\
\setlength{\inferLabelSkip}{20pt} % <<<<<<< added
\infer[(\implies I)]
{
(q \land r \land ¬s ) \quad \implies \quad ( u \lor r ) %changed <<<<<<<<<<<<
}
{
\infer[(\lor I r)]
{
\\u \lor r
}
{
\infer[(\land E_{2} r)]
{
r
}
{
q \land r
}
}
}
\end{document