The Niners' top three selections from the 2011 draft have been involved in off-the-field situations in recent weeks, resulting in a negative hit for the team's image. Most notably, star linebacker Aldon Smith was arrested at an airport last month and authorities say he used the word "bomb."
Quarterback Colin Kaepernick was linked to a Miami police report involving a woman who passed out in a hotel and later woke up in a hospital not knowing how she got there. Kaepernick has strongly denied any wrongdoing.
Cornerback Chris Culliver who made anti-gay remarks before the 2013 Super Bowl has pleaded not guilty to misdemeanor hit-and-run charges and felony possession of brass knuckles from a March 28 arrest.
"It's a risk-reward business," Baalke said. "And we try to take chances calculated chances and it has worked in a lot of cases. There are other times when the character of an individual coming into the NFL was sterling. But they end up being guys who get in trouble.
"It's not always the guys that come into the league with a checkered past that leave the league with a checkered past. It can be the opposite. And if anybody in here has the answer about who is going to end up doing what, give it to me. I could use it."
Here are five things to watch for in the draft for the 49ers, who pick 30th:
FRONT-OFFICE TEAMMWORK: For anybody wondering whether Baalke and coach Jim Harbaugh will be duking it out in the draft room about which player to take, the GM says enough already.
He insists the issue has been "misrepresented" since news broke that the Browns tried to trade for Harbaugh after San Francisco's loss in the NFC championship game.
"To say that it's always two rams butting heads is so false and misleading. To say there's no tension would also be false and misleading. It's good tension, it's creative tension. It couldn't be better," Baalke said. "I feel good about where we're at. If you want us to hug and mug for the cameras and do all that, you're looking at the wrong two guys."
TRADING UP: Don't put it past this team to move up the board. And Baalke just might look to make a splash with a player who could have an immediate impact for the Niners as they begin a new era at Levi's Stadium next to team headquarters.
He has done so before.
"A lot of it's spontaneous, happening as the draft's unfolding," Baalke said.
DEPTH AT LINEBACKER: San Francisco will be without All-Pro linebacker NaVorro Bowman for a while as he recovers from torn ligaments in his left knee sustained in the postseason loss to the Seahawks.
Baalke knows Smith could face a suspension from the NFL, too. The 49ers went 5-0 during Smith's five-week stint in rehab for substance abuse last season following his DUI arrest.
While Dan Skuta and rookie Corey Lemonier emerged as solid replacements for Smith's pass-rushing presence on the edge, San Francisco is expected to search for depth at linebacker. Michael Wilhoite also became a reliable reinforcement, and Baalke says the team is "very confident in being able to replace guys when they go down."
"We saw it in play last year," Baalke said. "Sometimes when you lose a player, you can't replace him with just one. Sometimes it takes multiple people, it takes other people stepping up to the challenge."
THE CORNERBACK NEED: Carlos Rogers and Tarell Brown joined the Raiders on the other side of the bay. With Culliver working to come back from a serious knee injury, drafting a cornerback will be a top priority to complement Tramaine Brock.
FINDING GOOD GUYS: All eyes will be on Baalke, who has a successful run of draft picks who have produced right away, including first-rounders Anthony Davis, Mike Iupati and Eric Reid. But now, at least some fans will be counting more than ever on the 49ers finding just the right player.
Baalke points to the locker room and roster as a whole, because only a few are affecting the franchise's reputation.
"We just have to do a better job. And that's the mentality of this group and that's the mentality of this ownership. To think that we don't care? I take offense to 'classless' or 'lawless,' because that's far from the truth," Baalke said. "Respect the masses because the masses are doing it right, and we'll get the other things fixed."