I have never worried about this before, as I only use inline (* -- *) comments for small comments or code for comments. If I need a multi-line comment, I would split my code into smaller parts and use text cells.
However, you can try using \[AlignmentMarker] in the rightmost *) :
1 + 2 + 3 + (* First three \[AlignmentMarker]*) 4 + 5 + 6 + (* Next three \[AlignmentMarker]*) 7 + 8 + 9 (* Last three \[AlignmentMarker]*)
Displayed as

Edit in response to comment:
If you have comments between the code (without the code on the left), then perhaps put it in a GridBox (created using Ctrl-Enter and Ctrl-, ), which is commented out using (* ... *) in a white font.

It is hard to give the code to do the above ... but here is the Box form:
Cell[BoxData[ RowBox[{"Manipulate", "[", "\[IndentingNewLine]", RowBox[{RowBox[{RowBox[{"a", " ", "=", " ", RowBox[{"x", "+", "1"}]}], ";", "\[IndentingNewLine]", " ", RowBox[{StyleBox["(*", FontColor->GrayLevel[1]], "", GridBox[{{"(*", RowBox[{"Inter", "-", RowBox[{"code", Cell[""]}]}], "*)"}, {"(*", "comments", "*)"}}, GridBoxAlignment->{"Columns" -> {{Left}}, "ColumnsIndexed" -> {}, "Rows" -> {{Baseline}}, "RowsIndexed" -> {}}], " ", StyleBox["*)", FontColor->GrayLevel[1]]}], "\[IndentingNewLine]", RowBox[{"{", RowBox[{"a", ",", SuperscriptBox["a", "2"]}], "}"}]}], ",", "\[IndentingNewLine]", RowBox[{"{", RowBox[{"x", ",", "0", ",", "1"}], "}"}]}], "]"}]], "Input"]