Yes, Ivanova and Talia Winters were always slated to be a sexually active lesbian couple;
JMS told Sci-Fi Universe (March 1996)
"We had it growing since the very first episode of the first season. The relationship was about all of that mutual antagonism that really means they're attracted."
Andrea Thompson (who played Winters) stated in "Creating Babylon 5" that:
"There was a sexual relationship between Talia and Commander Ivanova. It was edited so that it was not blatant. But that was exactly what happened. It had been talked about from the very beginning" (The Creating of Babylon 5).
An SFX Interview in July 1997 showed that they wanted to explore the relationship further
"I think that if Andrea Thompson had not left, we would have definitely explored the relationship further. That was the intention, but because she wanted to get out, we had to wrap it up quickly"
Claudia Christian also made it abundantly clear that her relationship with Talia was based on a mutual sexual attraction:
"I'll be quite honest, I was like the lesbian poster child; I got a lot of people writing to me from the armed forces and so forth, who loved the fact that they thought I was going to be gay. I'm not gay in real life, and I don't think I'm gay on the show, but I definitely think she had some kind of thing with Talia. I think a lot of gay women were hoping for that, and I didn't want to disappoint them; I thought it would be fun... Then Andrea left the show, so that's why it never came to fruition. The only reason it didn't go further is because we had to get rid of the character because Andrea wanted to leave. It could have been a long relationship." The Official Babylon 5 Magazine : June 1996
JMS (on the excellent Midwinter website) made it clear that they were involved with each other both sexually and on an emotional level;
Susan and Talia had been dancing around one another for months; that night [e.g. Divided Loyalties}, though, would've been the first time they got physically intimate.