Don't lose too much sleep over it. The conventional wisdom in this area is not very reliable, for a variety of reasons. IANAL but am studying to that end, and being a Euro I was already interested in immigration law.
I would say the USCIS website itself is a good source of general information for the immigrant/family. After long being criticized as overly bureaucratic and unhelpful they've made a lot of 'customer service' type changes - for example, there's a tool to look up the status of petitions online which is quite new. The latest thing is provide more assistance to people being naturalized, eg via http://www.uscis.gov/portal/site/uscis/citizenship which got a big makeover just in the last few weeks. Previously the would-be citizen's contact with the agency leading up to naturalization consisted of submitting forms, getting fingerprinted, and having to take the US civics quiz.
Anyhow, separating a couple during the interview typically only happens at a second interview when the USCIS officer (not agent) has specific reasons to doubt the veracity of the relationship - the couple hardly seems to know each other, or their filings are contradictory etc. If they have doubts after the first interview they usually issue a Request For Evidence inviting more documentation/clarification. Policy is to adhere to a neutral rather than skeptical stance by default, and proceed using an evidence-based methodology - challenging or accusing people at random is just going to result in complaints and slows everything down.
Merely applying doesn't put you under 'suspicion,' it's just a process of verification. The FBI does a fingerprint match and checks against the person's name in national and international law enforcement databases - this takes a while just because there's a lot of applications to work through. Most people are legit of course, so then it's just a process of going through the form evaluating the credibility and general stability of the applicant, verifying the authenticity of their marriage certificate/professional qualifications, medical reports etc. etc.
Now when they do suspect fraud, sure they might lie to see if they can catch a person out - as is true of any police interview. But it's not the default position. ICE agents (who go out looking for workplace violations etc.) are a different kettle of fish. There was a fuss at the end of last year about agents Utah in dressing up as Mormon missionaries.