Kimber -- I have had no problems stitching exactly on the seam of my open pressed seams. My piecing stitches are quite small, my quilting stitches are larger. In both instances I use fresh sharp needles. I have had very very few stitches ever break, I mean count on my hands total not just on one top but on all of them in 20 years. Just like when you are piecing you are not punching holes in the fabric you are slipping between the weave, change your needles often and you shouldn't have problems.
I can see where if the stitch length is too long that quilting in the ditch might aid batting in escaping through the seams or other problems. All I can say is I haven't found it to be a problem even after years of hard use and heavy washing (dust mite allergies, all my old quilts had years of being washed monthly).
Last year I did my first ever quilt with the serpentine stitch. My vintage machine didn't give me that option, but my modern one does. I think it is an easy, versatile, and yes, stabilizing method of quilting that works very well with a lot of the modern large/grid type quilts. I think I would deliberately use it if I was concerned about how securely a border was sewn on a quilt, even if did quilt the rest of the quilt differently -- so in that case I think it would enhance rather than hurt the seams.