One thing I did to make the today marker a little less obtrusive, was to edit the xml/calendar.xml file and change the <today> element to have layer="-10".
It should look like this when you are done:
<appearance layer="-10" element="bitmap.today" align="CENTER" />
This places the today marker behind all of the other elements in the calendar (like the date number, the event bitmaps, etc.)
One thing to note though, is this fix only works the type of calendar that you change it on.
For instance, if you change the xml/calendar.xml file, then switch to the long calendar format, the edit will not be shown. To fix that one, you will need to change the xml/long calendar.xml file to fix it for that format. The same goes for the other calendar types that you might be using.