If you take a look at the Combinatorica package in Mathematica8 in (mathematicapath)/AddOns/LegacyPackages/DiscreteMath/Combinatorica.m you wi
I am currently working on rewriting your ApplicationMaker for newer Mathematica-Versions with added functionalities and came to the exact same question here.
My answer is simple: Mathematica dont allowes you to use formated summaries for your symbols (or even build in symbols), so we have to unformate the usage-strings for the summaries. The usagestring itself can still have formatting, but one needs to have a function that removes all the formatingboxes from a string.
i have a solution that uses the UndocumentedTestFEParserPacket as described by John Fultz! in this question.
This funny named Tool parses a String Input into the real unchanged Mathematica BoxForm.
This is my example code:
str0 = Sum::usage
str1=StringJoin[ToString[StringReplace[#, "\\\"" -> "\""]]& /@
(Riffle[MathLink`CallFrontEnd[
FrontEnd`UndocumentedTestFEParserPacket[str0, True]]〚1〛
//. RowBox[{seq___}] :> seq /. BoxData -> List, " "]
/. SubscriptBox[a_, b_] :> a<>"_"<>b
/. Except[List, _Symbol][args__] :> Sequence@@Riffle[{args}, " "])];
str2 = Fold[StringReplace, str1,
{((WhitespaceCharacter...)~~br:("["|"("|"=") ~~ (WhitespaceCharacter ...)) :> br,
((WhitespaceCharacter ...) ~~ br:("]"|"}"|","|".")) :> br,
(br:("{") ~~ (WhitespaceCharacter ...)) :> br,
". " ~~ Except[EndOfString] -> ". \n"}]
and this is how the Output looks like (first Output formatted fancy str0, second simple flat str2)

Code Explanation:
str0 is the formatted usagestring with all the StyleBoxes and other formatting boxes.
str1:
UndocumentedTestFEParserPacket[str0, True] gives Boxes and strips off all StyleBoxes, thats because the second argument is True.
First Replacement removes all RowBoxes. The outer BoxForm changed to a List of strings. Whitespaces are inserted between these strings the by Riffle. SubscriptBox gets a special treatment. The last line replaces every remaining FormatBox such as UnderoverscriptBox and it does that by adding Whitespaces between the arguments, and returning the arguments as a flat Sequence.
ToString[StringReplace[#, "\\\"" -> "\""]]& /@
was added to include more cases such as StringReplace::usage. This cases include string representations "" with Styles inside of a the usage-string, when "args" has to be given as strings.
str2:
In this block of code i only remove unwanted WhitespaceCharacter from the string str1 and i add linebreaks "/n" after the ".", because they got lost during the Parsing. There are 3 different cases where WhitespaceCharacter can be removed.
1 removing left-and right sided WithespaceCharacter from a character like "[".
2. and 3. removing WithespaceCharacter from left(2) or right(3) side.
Summary
Istead of summary-> mySymbol::usage, use summary -> unformatString[mySymbol::usage] with unformatString being an appropriate function that performes the unformating like descriped above.
Alternatively you can define another usage message manually like
f::usage = "fancy string with formating";
f::usage2 = "flat string without formating";
than use summary -> mySymbol::usage2