Microsoft includes an example using an ISAPI filter to all outbound cookies: http://msdn.microsoft.com/en-us/library/ms972826
or URL rewriting could be used http://forums.iis.net/p/1168473/1946312.aspx
<rewrite>
<outboundRules>
<rule name="Add HttpOnly" preCondition="No HttpOnly">
<match serverVariable="RESPONSE_Set_Cookie" pattern=".*" negate="false" />
<action type="Rewrite" value="{R:0}; HttpOnly" />
<conditions>
</conditions>
</rule>
<preConditions>
<preCondition name="No HttpOnly">
<add input="{RESPONSE_Set_Cookie}" pattern="." />
<add input="{RESPONSE_Set_Cookie}" pattern="; HttpOnly" negate="true" />
</preCondition>
</preConditions>
</outboundRules>
</rewrite>