Will the treatment for an HIV cure have side effects? 

No one knows. When combination therapy was introduced in 1996, it took at least five years before the worst side effects (atrophy, neuropathy, hallucinations, nausea, diarrhoea) were filtered out. But the need was much greater then than it is now. Back then, if you didn't take the pills you would die. So a balance must be found between how many side effects you are willing to tolerate for a cure and how many side effects you currently have from your HIV medication.