If it was specified by a matrix I guess you can't with a straightforward way, but you can easily parse the value:

var matrixRegex = /matrix((-?d*.?d+),s*0,s*0,s*(-?d*.?d+),s*0,s*0)/,

    matches = $(element).css('-webkit-transform').match(matrixRegex);

matches[1] will contain scaleX and matches[2] will contain scaleY. If it's possible that other transformations have also been applied, you'd need to slightly tweak the regex, because now it assumes that all other parameters are 0.

A way to just get the scale values might be to remove any transforms, measure the computed width/height of the element and then add them back and measure again. Then divide new/old values. Haven't tried it, but it might work. jQuery itself uses a similar approach for many measurements, it even has an undocumented $.swap() function just for this.

PS: You are using -o-transform -moz-transform and -ms-transform too, right?