In the case of INVISIBLE LETTER, it seems likely -- based on the comments of experts -- that the benefits outweigh the disadvantages. But new control characters (and quasi-controls like IL) have tended to cause more problems and confusion for Unicode in the past than new graphically visible characters. The possibility of misuse has to be evaluated, and the rules do have to be stated clearly. Combinations involving IL plus SPACING ACCENT, or IL plus ZW(N)J, or whatever, should be part of the rules; what effect should such combinations have, and are they discouraged? For IL, that is probably good enough.
The most important misuse of IL could be avoided by saying in the standard that a renderer should make this character visible if it is not followed by a combining character that it expects. This would avoid possible spoofing by including it within some critical texts such as people and company names in signatures. A candidate rendering would be the dotted circle and square as seen in the proposal, or a dotted square with "IL" letters inside. This glyph would appear even if "visible controls" editing mode is not enabled.

