Found you can tweak the crossover between windows sens and ingame. these settings will get your mouse doing what you want when you want it.
Another command which might be useful for sniper is the pitch and yaw settings.. lower up and down to side to side sens ratio to keep at head level ;)
(haven't tried these myself in TF2 but used to tweak a lot of these exact commands in q3)
m_customaccel : 0 : , "a", "cl" : Custom mouse acceleration: 0: custom accelaration disabled 1: mouse_acceleration = min(m_customaccel_max, pow(raw_mouse_delta,
m_customaccel_exponent : 1 : , "a", "cl" : Mouse move is raised to this power before being scaled by scale factor.
m_customaccel_max : 0 : , "a", "cl" : Max mouse move scale factor, 0 for no limit
m_customaccel_scale : 0 : , "a", "cl" : Custom mouse acceleration value.
m_filter : 0 : , "a", "cl" : Mouse filtering (set this to 1 to average the mouse over 2 frames).
m_forward : 1 : , "a", "cl" : Mouse forward factor.
m_mouseaccel1 : 0 : , "a", "cl" : Windows mouse acceleration initial threshold (2x movement).
m_mouseaccel2 : 0 : , "a", "cl" : Windows mouse acceleration secondary threshold (4x movement).
m_mousespeed : 1 : , "a", "cl" : Windows mouse acceleration (0 to disable, 1 to enable [Windows 2000: enable initial threshold], 2 to enable secondary threshold
m_pitch : 0 : , "a", "cl" : Mouse pitch factor.
m_rawinput : 0 : , "a", "cl" : Use Raw Input for mouse input.
m_side : 0 : , "a", "cl" : Mouse side factor.
m_yaw : 0 : , "a", "cl" : Mouse yaw factor.