Pietersen returned to South Africa today having met with Cook and other England players as part of his agreed programme of reintegration into the national team.
The flamboyant batsman has not played for England since the text message affair erupted at the end of the summer Test series against South Africa.
Cook, England's Test and one-day captain, said no decision has yet been taken about whether Pietersen will be added to the squad to tour India.
Although he conceded time was running out given England leave next Thursday, Cook stressed it was more important to make the right decision than a quick decision.
England face India and New Zealand this winter and then host the ICC Champions Trophy next summer before defending the Ashes against Australia.
''The meetings have been going on and the process is well underway,'' Cook said.
''We do need to draw a line in the sand at some stage and move forward for the sake of English cricket.
''We need to move forward as a team. We have an amazing 18 months ahead of us. We all know how important team harmony is and team ethos is and that showed when we were successful, how tight we were as a side.
''That is a very important thing to make a good side.
''It is important we don't rush this process so we get the best opportunity of that. We want all our world-class players playing for England.
''We have got to get it right. It is a very important decision for the sake of the England team moving forward. We have got to be thorough.''
Cook said England's performance at the Twenty20 World Cup had not strengthened his resolve to get Pietersen back involved.
But he conceded the side, led by Stuart Broad, had missed some experienced heads.
Pietersen was not considered for selection while the likes of Cook, Matthew Prior and James Anderson do not feature in England's Twenty20 plans.
''If we are being totally honest, sometimes the inexperience probably showed in certain circumstances (in Sri Lanka),'' Cook said.
''As a side you are always looking for your senior players to step up to the mark and the senior players weren't there.''
England will host the final Champions Trophy next June before it is scrapped to make way in the international calendar for a new World Test Championship from 2017.
Cook has led England to the top of the one-day rankings but he insisted there is much more to come from his team.
''We don't feel like we are the number one. We have a huge amount of potential and work to do,'' he said.
''The Champions Trophy is is a very important event for us as a side. We don't often get the opportunity to play at home in a tournament. We have only won one ICC tournament and we would love to win another.
''We have a great winter in India and New Zealand, the ICC Champions Trophy and then Australia. We have the opportunity to do something special if we play well.''