I don't think it is a good idea to separate CS (or SE) from engineering, because there are core principles of engineering upon which it (they) rest. In my own personal experience, the study of linear systems theory and probability was key to my ability to implement algorithms that enabled fair sharing of resources in computer networks and distributed systems. (I'd also like to add that women such as Sally Floyd are core contributors to this subdiscipline of CS.) This doesn't mean there is no place for selected topics in CS (or SE) that can be applied to other disciplines; in fact, many disciplines such as bioinformatics draw on such topics.
WRT the meritocracy of CS, there is a justified reason for this: computer software runs on real systems that require real resources. I don't feel there is an anti-female or anti-feminist agenda here. The way that the arguments for or against certain design choices are articulated is often criticized as anti-female. I agree and think this is unfortunate. It has no doubt driven many promising women out of the field.
Whether CS (or SE) is a "real" engineering discipline is a highly contentious topic. Given what has happened to the industry of late - jobs have been lost in the US to low-income, low-wage countries, licensing and certification has been proposed as a solution. There is backlash to this argument, claiming that certification does not imply qualification, and that it stifles innovation. But the software industry does not currently have a way of articulating to those outside of the industry what it should be expected to do.
I don't have any good ideas on how to encourage women to pursue CS (or SE). In all honesty, I can't fault any woman for choosing another field, given the loss of long-term viable career options, the high stress, etc. However, in other countries, especially the low-wage, low-income countries I mentioned earlier, this seems to be much less an issue. In these countries, there is parity in numbers between women and men. An argument I've heard from Jane Margolis is that these women see entrance into the software industry as a means of economic liberation. Women in the US have more options, and exercise them.