The 24-year-old Smith was arrested April 13 at Los Angeles International Airport for a fake bomb threat, and officials in L.A. are pondering misdemeanor charges. Smith also will face felony gun charges and a drunken driving charge at a Santa Clara County courthouse Tuesday.
The 49ers must decide by May 3 whether to exercise a $9.75 million option on Smith for the 2015 season, although ESPN NFL Insider Adam Schefter recently reported the team isn't expected to do that. If they don't, but decide later that they'd want Smith back in 2015, the 49ers would have to give him a long-term deal or apply the franchise tag on him, which would likely be in the $12 million-$13 million range.
Baalke said the team is still mulling the decision, but made it clear the 49ers don't want to "toss" Smith out.
Asked if he hopes Smith will play this season and in 2015, Baalke replied: "And in 2016 and 2017 and 2018 ... You don't just open the door and toss people out."
Baalke said several times that the team is "disappointed" in Smith's continued missteps and that "they have to stop."
He said Smith is working daily to improve himself off the field and is working with the team during its offseason conditioning program.
When asked what he wants to see from Smith, Baalke said: "Growing. Starting to understand, starting to realize the importance of his own accountability."
Meanwhile, Baalke continues to monitor the ongoing investigation in Miami involving quarterback Colin Kaepernick and receiver Quinton Patton. Both are part of an ongoing investigation in a "suspicious" incident there, although police have yet to name either as a suspect in a criminal case.
"To say there's no concern would be a misrepresentation," Baalke said of the investigation. "We're always concerned, but let's let this thing play out and see where it goes."
Kaepernick is entering the final year of his contract. Baalke said at the NFL owners meetings last month that the 49ers would like to get a deal done before training camp.
He stepped off that goal Friday.
"Negotiations of these are long, can be drawn out, can be tedious," Baalke said. "It takes a lot of work, thought and engineering."
Baalke disputed any talk that he is running a "lawless" organization, and he spoke passionately about his players and twice said the locker room is filled with "good men."
"Respect the masses because the masses are doing it right," said Baalke, "and we'll get the other things fixed."