It seemed only appropriate that Safe Schools founder Roz Ward was flanked by rows of flags as she returned to work.

Just days earlier, La Trobe University suspended the controversial academic after she called the Australian flag "racist" on her private Facebook page and jokingly said it should be replaced with a red flag.

But the flags that fluttered in the icy wind on Monday morning were purple and stamped with the National Tertiary Education Union's logo.

Academics, unionists and students cheered as Ms Ward held her clenched fist in the air, and marched through a guard of honour into the university's CBD campus.

"This is about more than me and my experiences," Ms Ward told her supporters, who were clutching "We Stand With Roz" signs. "Homophobia and transphobia are very much alive in young people's lives," she said.

"We are trying to do something about it, but there are a lot of people that are trying to stop us from doing that work." But Ms Ward stopped short of criticising the university.

The saga is not yet over.

The union is still considering legal action against La Trobe, which it has accused of tarnishing Ms Ward's reputation.

They are also considering action against former Victorian premier and Beyond Blue chairman Jeff Kennett and The Australian newspaper – both vocal critics of Ms Ward.

Students and academics believe the saga has tarnished La Trobe's reputation, and claim the university's actions were an attack on academic freedom and freedom of speech.

"That's one of the ironies ... that was [La Trobe vice-chancellor John Dewar's] excuse for trying to sack Roz ... but the push back on him has made La Trobe a real embarrassment for a lot of people," Robin Laycock, an associate lecturer at La Trobe's school of psychology said.

National Tertiary Education Union Victorian secretary Colin Long said the university was more concerned about protecting its brand than supporting its community, who are entitled to controversial views.

"Universities seem to think they are corporations and businesses above all else today," he said.

Ms Ward spent her first morning back at work responding to emails which had been languishing in her inbox since her suspension on Wednesday.

Teachers had sent emails wanting support for transgender students, and inquiring about making their school formals more inclusive.

She said only a small minority of people think the Safe Schools program is controversial.

"The vast majority of people support the idea that LGBTI young people should feel safe and able to be themselves at schools," she said.

The program – which aims to promote acceptance of LGBTI students – has been running in Victoria since 2010 and has enjoyed cross-party support for most of its existence.

But it has recently come under attack, with Prime Minister Malcolm Turnbull announcing a review amid claims it aims to indoctrinates children with a "gay agenda".

The Victorian Opposition has promised to scrap the "politicised" program if it wins the 2018 election and replace it with an anti-bullying program.

Right-wing critics have seized on Ms Ward's political views – she's a Marxist.

But Ms Ward said she should not have to defend her political views.