[Editor's note: This story has been updated to reflect the mutual decision between Subway and Jared Fogle on Tuesday afternoon to suspend their relationship.]

As child pornography allegations circle around Jared Fogle—best known as weight-loss guru "Jared from Subway"—experts say the fast food chain runs the risk of tarnishing its reputation permanently if it doesn't handle the situation appropriately. However, with so much speculation and few hard facts, it might be smarter to pause before making any major decisions to completely sever ties.

Read More Subway, Jared Fogle suspend relationship amid child porn investigation

"It's a very tricky balancing act," said Will McInnes, chief marketing officer of social media analytics company Brandwatch. "There's 24 or 48 hours between the smoke clearing and reality emerging. There's not a great deal they can do but stay very close to the events as they unfold."

"The smart thing for a brand is to wait and see what occurs," added Ken Ungar, founder & president of U/S SportsAdvisors.

NBC affiliate WTHR reported that the FBI raided the Subway pitchman's home in Zionsville, Indiana, early Tuesday. The search warrant alleged that Fogle may be connected with a child pornography investigation, according to the report.

It follows the news the former executive director of the Jared Foundation, Fogle's organization that aims to combat childhood obesity, was arrested in April on child pornography charges.

Fogle did not respond to requests for comment.

Subway initially said earlier on Tuesday in an emailed statement to CNBC that they were "very concerned and will be monitoring the situation closely." Later that afternoon, the chain announced the two parties decided to suspend their relationship.

"Subway and Jared Fogle have mutually agreed to suspend their relationship due to the current investigation," a Subway representative said in an email statement to CNBC. "Jared continues to cooperate with authorities and he expects no actions to be forthcoming. Both Jared and Subway agree that this was the appropriate step to take."

Sarah Aitken, chief marketing officer of the Americas at creative advertising agency Iris Worldwide, said there is no harm in issuing a short statement that clarifies Subway is aware of the situation without denouncing its relationship with Fogle. To end things immediately could be seen as a negative, especially if any allegations end up to be unfounded.

It's important to note that the company is just halting their partnership at this time, meaning there is still a chance that the two could work together in the future.

"Whether he is guilty or not, Subway is currently being associated with child pornography, and so the most important thing to act on is to clarify that they take allegations of this nature very seriously with a short brand statement," Aitken said. "This isn't immediately cutting all ties with Fogle. It is saying that the brand of course stands against crimes of this nature and will help with any investigation if required."