The MathType support folks offered a partial remedy:
1) Close MathType
2) Open /Users/~home/Library/Preferences/MathType 6 Preferences with a text editor
3) In the {Windows} section, change the PicturePadding setting from 2 to 0.
Equations created after this fix will look substantially better. See the grab at
http://img18.imageshack.us/img18/6681/spacing2.jpg.
Unfortunately, the line spacing problem persists. In the second paragraph from the above image, line spacing is increased to 1.3. The presence of the equation unnecessarily alters the distance between the third and fourth lines. The problem remains no matter how high the line spacing is. In a document containing a number of inline equations, the net effect is awkward, "jagged" line spacing.
For comparison purposes, here's an example of the same text in LaTeX with line spacing set to 1.3:
http://img509.imageshack.us/img509/286/spacing3.jpg. The irregular line spacing is far less pronounced.