As said, toss in an NPC. I usually try to put one in that won't hog the spotlight. That's how my Giraffe shaman was born, who actually later turned into a PC. Like you, I had 2 players at the time and they had no magic at all. I purposely gave them a shaman who was more of a support/utility spell/stealth type, rather than a full on battle shaman. And the totem's tendency for avoiding combats, similar to Rat, made the character less likely to outshine the players, particularly in combat.
I think it's generally not a good idea to try to pay with 1, but 2 is definitely enough. 3 and 4 is optimal, and getting 6 or more can actually be difficult to run.
Go easy on them, but this pretty much goes even full sized teams. It's a deadly system and so be less worried about challenging than you are about keeping them alive. Particularly if you think they will see any auto fire or heavy magic. Try to avoid hammering them on areas they lack, especially at first.
Feel free to give them help. Have the Johnson give advice, plan and infiltration ideas, or throw in other help. Be more generous about information they find on the legwork portion, such as ways to infiltrate a sight, guards that are open to bribery or able to be blackmailed, etc.
The style of the game can also effect play. If it's more planning involved and there is less over the top heavy combats, the chances are better for a small team. Smal teams of Face/Infiltrator/Hacker types are particularly suited to this type of game.