How to set the LaTeX font size in inkscape?

You can simply add a latex specification for the font size. For example, you can use \fontsize in the "latex formula" box:

\fontsize{9pt}{1em} $\sum_{ij} w_{ij}$

Personally, I haven't used it yet, but the extension textext allows you to set an scale factor which:

(...) affects how much a newly created LaTeX object is magnified. You can later change/reset this via Object -> Transform -> Matrix.