I think you've got it wrong that the Relationship Calculator compromises the integrity of data. It only displays data and does not alter them. No data are in jeopardy.
I'm not sure you've been clear enough for me to understand which "Relationship Calculator" in 2012 you're talking about. When I see someone write this I think of the window that pops up when you select "Relationship Calculator..." from the tools menu. I gather from what you're saying, however, that you're talking about (1) the relationship that is used for the "Relationship Chart" in the "Publish" workspace or (2) the information pane of the "People" workspace that displays a selected person's relationship to the home person in the tree. I think you're talking about the former.
The Relationship Calculator under the tools menu provides a partially functional solution to the problem you've described. It is supposed to detect all possible relationships between two people, but it doesn't always work (especially for distant relationships). When it does detect a relationship, however, it gives you the option to generate a chart similar to the "Relationship Chart" from the "Publish" workspace, only you can't modify any of its options (like displaying thumbnails). For this reason, most of us temporarily detach and reattach people as necessary to force it to find the desired relationship for the chart. It's a real PITA.
I recommend that you contact email@example.com
to report this problem. The more they hear from us, the better chance of getting a fix.