Emacs org-agenda-list destroy my windows splits

Set org-agenda-window-setup in your init.el

(setq org-agenda-window-setup 'current-window) 

Thanks to quicksilver from #org-mode on freenode

Type C-h v org-agenda-window-setup for other options.

The simplest way is to use default Emacs customization:

M-x customize-group org-agenda-windows

There are several options, including current window. Try them out, I think one of them will do what you need.