How can I import and scale matplotlib plots, keeping fonts the correct size?

The matplotlib PGF backend saves as raw PGF. What you probably want instead is pgfplots, which you can get using tikzplotlib, assuming your plots aren't too complex and all the features are supported.

Sample Python script for creating figure:

from pylab import *
from tikzplotlib import save as tikz_save
x = linspace(0, 10, 101)
plot(x, sin(x))
xlabel('$x$-axis')
ylabel('$y$-axis')
tikz_save('fig.tikz',
           figureheight = '\\figureheight',
           figurewidth = '\\figurewidth')

Sample accompanying LaTeX document that brings in the plots with two different dimensions (you could use \input; I'm using \InputIfFileExists so that missing figures won't kill compilation):

\documentclass{article}

\usepackage{pgfplots}

\newlength\figureheight
\newlength\figurewidth

\begin{document}

\setlength\figureheight{2in}
\setlength\figurewidth{3in}
\InputIfFileExists{fig.tikz}{}{\textbf{!! Missing graphics !!}}

\setlength\figureheight{3in}
\setlength\figurewidth{4in}
\InputIfFileExists{fig.tikz}{}{\textbf{!! Missing graphics !!}}

\end{document}

Output:

Depending on what you are doing, you could also consider using my PythonTeX package to put everything in the LaTeX source:

\documentclass{article}

\usepackage{pgfplots}
\usepackage[stdout=false]{pythontex}
% matplotlib2tikz prints messages to stdout, so don't include
% stdout automatically; could also redirect stdout to avoid this
\setpythontexworkingdir{.}
% set PythonTeX to use the document root directory as the working
% directory, so that all plots will be saved there; could use 
% another location, but then would need to specify a path when
% using \input and \InputIfFileExists

\newlength\figureheight
\newlength\figurewidth

\begin{document}

\begin{pycode}
from pylab import *
from tikzplotlib import save as tikz_save
x = linspace(0, 10, 101)
plot(x, sin(x))
xlabel('$x$-axis')
ylabel('$y$-axis')
tikz_save('fig.tikz',
       figureheight = '\\figureheight',
       figurewidth = '\\figurewidth')
\end{pycode}

\setlength\figureheight{2in}
\setlength\figurewidth{3in}
\InputIfFileExists{fig.tikz}{}{\textbf{!! Missing graphics !!}}

\setlength\figureheight{3in}
\setlength\figurewidth{4in}
\InputIfFileExists{fig.tikz}{}{\textbf{!! Missing graphics !!}}

\end{document}