There is no reason using a plugin should affect your SEO in any noticeable fashion…those plug-ins are not perfect any how, if you REALLY need it, you need to send your content to a professional translator and create separate setups for each respective language…That would in fact help your SEO.
How do you mean a seperate setup? I thought about that, but how do you have more than one homepage with wordpress? Do you mean a seperate wordpress installation for each language?
I suppose the problem is, you can´t specify different title and meta tags unless it is in fact a different page….that´s the problem with plug-ins like Qtranslate. Simple google translate plug-ins look naff as well.