Make Syntastic close just the error window

Syntastic uses the location list (a window-local variant of the quickfix list), so a :lclose will close it, but keep the other buffers.

As per syntastic's help pages, the initial height can be configured:

:let g:syntastic_loc_list_height=5

But I suspect that your intrusive Janus distribution has a hand in that. Vim "distributions" like spf-13 and Janus lure you with a quick install and out of the box settings, but you pay the price with increased complexity (you need to understand both Vim's runtime loading scheme and the arbitrary conventions of the distribution) and inflexibility (the distribution may make some things easier, but other things very difficult). Vim is incredibly customizable, using someone else's customization makes no sense.

The command to close the Syntastic error window is:

:SyntasticReset