Smith was arrested earlier this month having made false claims to be carrying a bomb at Los Angeles International Airport, while he is also currently facing felony gun charges and a drink driving charge.
The 49ers have until May 3 to decide whether to exercise the fifth-year option in the 24-year-old's contract, but while they have not yet made that decision, Baalke hinted that he saw Smith's long-term future in San Francisco.
Asked if he hopes Smith will play this season and in 2015, Baalke told reporters: "And in 2016 and 2017 and 2018. You don't just open the door and toss people out."
Smith will face his felony gun charges and the drink driving charge on Tuesday.