Make it easy on yourself and set up an ssh config. It might be worth using Cygwin

On my Windows 7 box I use Cygwin in precisely that way for ssh connections to various nix machines. It works well. I envisage that it would also work equally well from an MSYS2 installation.

For scripted communication between Windows and nix I usually use Net::SSH2 or Net::SSH::Any (which utilizes Net::SSH2 via a more user-friendly interface), run from a native Windows cmd.exe shell.

Cheers,
Rob