I'm really glad it didn't get worse. But please don't push yourself just yet.
Literal
Truly not-aggravating good-was. But still overdoing not-do [manner-ように] please.
こじらせなくて良かった — こじらせる means 'to aggravate, make worse' (especially an illness). ~なくて良かった is the relief pattern: 'I'm glad it didn't happen.' まだ無理はしないように is a gentle prohibition: 無理 ('pushing too hard') + しないように ('in a way that doesn't'). The sentence pair captures the Japanese concern pattern — relief followed by continued care instructions.