Whitney's definitely a step up in difficulty, but I think it's not too surprising that the always-female Pokémon with decent stats and Rollout and Attract would be tough for people whose team's ace was likely to be a predominantly male Fire-type. I actually have a few ways around that Miltank these days.
1: Pick Chikorita as my starter and reset for a female. This makes that thing a joke. I am not kidding. Being female invalidates Attract, and Bayleef can weaken Rollout and Stomp with Reflect, and set up Poison Powder to chip away at Miltank's HP (and burn through that pesky Lum Berry if you're playing HGSS). From there, Bayleef can either severely wear down Miltank for the rest of your team, or else just outright take it out herself. I've seen it go either way.
2: In Crystal specifically, buy a Wobbuffet from the Game Corner. Legit the best 1,500 coins you will ever spend. You'll want to level it up just a little bit- it comes at level 15, and Whitney's Miltank is level 20, so you'll want to at least lessen that gap somewhat, even if you're not up to closing it completely. But it pays off. Just wait for the Rollout to begin, switch to Wobbuffet, and spam Counter until Whitney cries. And Wobbuffet's usefulness doesn't end here, either- with the relatively simple movesets and AI back then, it's actually usually fairly easy to know whether to go for Counter or Mirror Coat in a lot of battles. And in a pinch, Destiny Bond on some of the rougher enemies, like Morty's Gengar, can be absolutely clutch.
