I don't think "so far, so good" implies that something will go wrong later, not nearly as much as it implies it does that something can go wrong later.
I might use those words to describe the status of a major project that appears to be on-time, or a to report progress on a long trip that has been without incident.
As for applying it to a sonogram, I'll admit, maybe that's not the best choice of words. Then again, maybe the technician interpreted the question differently. By asking, "Is everything okay?" your wife may have meant, "Does the baby look healthy?" but the technician may have interpreted it as "Is all the equipment working fine?" or "Is the image clear?" or even "How has your day gone so far?" After all, after a technician has performed a dozen of these per day, week after week, month after month, he's probably encountered all sorts of technical problems.
As I said, maybe not the best choice of words, but I doubt very much that he intended to sound ominous.