1) Go to the Church immediately at the start. (You will need 3 coins to do this. If you don't have coins, not to worry, there's three of them on a table at the cafe if you start there, and there's another 3 on a table by a sleeping guy near the Church)
2) The Redheaded Scientist will enter to start confession as you walk near her. Note her black suited bodyguard nearby. There's guys like this deployed around the Church and Harbor to supposedly guard the contaminated dead Scientist in the Church Morgue.
3) Let the Scientist finish her confession.
4) When she leaves, enter her confessional booth and quickly throw a coin inside the confessional booth's corner. Exit the Confessional and get out of sight of the Bodyguard who will attempt to investigate inside the Confessional.
5) Enter the Confessional and Subdue this Guard. No one can see you inside, and with this NPC occupying the Confessional, no one else will attempt to go inside ever again. (Note: At the very beginning you can actually bum rush the Redhead Scientist inside this same Confessional and Subdue her immediately to get the Keycard and Dongle but the Bodyguard will eventually find her KO-ed in here, ruining SA)
6) Exit the Confessional and run across the Altar and continue out of the side door of the Church. You will see the Morgue, turn left towards the graveyard then right where you should see the double-doors main back entrance of the Morgue and another Man-In-Black.
NB: At this point,the Redhead Scientist will make two stops before going to the Morgue. She'll pray at the Altar, and then pray at the candles near the side door exit. You have to hurry a bit.
7) Continue past them where you will see the staircase leading to the Sewers. Throw a coin down the stairs and hide. (Keep tabs on the Redhead's position. She should be at the Candles near the Side Door of the Church).
8) When the MIB Morgue Guard goes down the stairs past you, sneak into the Morgue's backroom (with the Open Coffin) and wait. The Redhead should be heading for the Morgue's back door where you just came in.
9) If the Guard you led down the stairs has not returned, simply dupe the Redhead into the Open Coffin Room with a coin. Subdue her, pick up the Lab Keycard and Dongle, then drag her straight into the Morgue and hide her in a Box.
10) Leave with SA/SO run still intact, and with Lab Keycard and the Virus Dongle. You can also pick up the Bouquet of Flowers beside the Open Coffin if you want a little something extra. 99% of the time the Morgue Guard only just comes back at this time and is not the wiser when you walk out of the Morgue to escape Trespassing.
N.N.B.: If the timing is slightly off after Step 6, the Morgue Guard you duped into going down the stairs may come back earlier and he'll have an argument with the Redhead saying she's not allowed to go in there, but she'll eventually be allowed in. There is also a Priest who pops in through another set of double-doors to bless the Open Coffin whenever things go longer than expected. Just adjust accordingly.