In SSIS you can use the DATEPART function. So, even though it would be a little more code that you might want, you can concatenate all the separate parts you want. (I'm fairly certain there is a better way though)
(DT_WSTR,2)DATEPART( "hh",GETDATE() ) + ":" +(DT_WSTR,2)DATEPART( "mi",GETDATE() ) + ":" +(DT_WSTR,2)DATEPART( "ss",GETDATE() )
As far as I am aware, there isn't a built in function which will convert your date time (with miliseconds) to a date time to only seconds. Like the following would. :
SELECT CONVERT(VARCHAR(20), GETDATE() ,20)
Personally, I'd put the whole datetime stamp into the end table then run some further conversion against it if SSIS can't do it.
for a little more on this