If M0 and M1 are your rotation matrices in the previous and the current frame, then they are related by:

R*M0 = M1 (1)

where R is a rotation matrix.
From (1), you get that

R = M1*transpose(M0)

From http://en.wikipedia.org/wiki/Rotation_matrix:

R(0,0) + R(1,1) + R(2,2) = 1+2*cos(w) (3)

where w is the angle of the rotation, divide it by your delta, you get the angular velocity.

There is one problem though, the number of solutions to (3) is infinite, which means that strictly speaking, it's impossible to do what you are trying to do. In practice, I guess you can assume that abs(w) is small, so you can choose the smallest solution.

I just found another article on wikipedia which will help you, see section "Log map from SO(3) to so(3)".

The formula is:
w = 1/2sin(theta) * [R(3,2)-R(2,3); R(1,3)-R(3,1); R(2,1)-R(1,1)]

I have not checked the it, but I suspect an error in their formula. It's surprisingly almost symmetrical, but not quite... I wonder if the last R(1,1) should read R(1,2)?