You might be able to customize the makePseudonyms function in /etc/e-smith/events/actions/update-user-pseudonyms, plus any changes in the main body of the program if you want to avoid creation of two pseudonyms for every user.
I don't think there's any official way to modify this file, so you'll be moving "off the reservation": your changes will evaporate with each update to e-smith-email (e-smith-email-5.2.0-25.el5.sme.noarch on my SME 8.1 server)
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The smallest change you could make would be to replace the underbar_pseudonym with your desired value in line 59:
Current line 59: $underbar_pseudonym =~ s/\./_/g; # Change dots to underbars
Possible alternative:$underbar_pseudonym =~ s/\.//g; # Change dots to nothing