There's an interesting post on the Feminist SF Blog about aliens in Larry Niven's Known Space series. Essentially it points out how both the Kzinti and the Puppeteers both have what amount to non-sapient females, and how this amounts to a stealth misogyny. An interesting point that I think goes a little off the rails when the argument turns to objections to the biological justification of the Kzinti's sexual dimorphism:
I presume Niven had been asked earlier why all the kzinti who we ever met in Known Space were all males, and he was trying to come up with a backstory to excuse this other than “I’m a sexist git, what can I say?”
Actually, it's more like Niven mentioned the Kzinti sexual dimorphism in an early Known Space story and was pretty much stuck with it whenever he wanted to return to the species. But the point isn't the biological rationale, but the authorial rationale. Now I'm not going to try and step into Niven's head here, but he did offer up a case study in how world-building (and by extension, alien-building) is a political statement, whether you want it to be or not.
This isn't to say you can't play with reproductive issues with your aliens, after all, changing the way a species produces young is one of my top three ways to make a species feel alien. (The other two are altering the primary mode of sensory input, and changing how they communicate.) The thing you need to bear in mind (to minimize the possibility of a feminist SF geek calling you a sexist git) is the fact that when you change aspects of reproduction, and the society that results from the change, you are making implicit statements about how human reproduction affects society. When you create gender roles for an alien species, you are making statements about gender roles in general. If you aren't aware of what you're doing you could end up being blindsided by people making interpretations of your text (maybe even you) that you didn't intend.