Yes, the prohibition really is inhibiting intra-party dissent by and large.
However, in my view, it's not equivalent to the whip voting instead. Should members of a party rebel in a large group and they get expelled, the party whip loses their votes (until by-elections or similar), so is not the same thing as if the whip could just vote instead of the MPs/MLAs.
Furthermore, the rules actually allow a substantial part of parliamentary group of a party to merge with another, without any expulsions. It's actually a bit more controversial what should happen if the defections happen to reach that threshold, but don't happen all at once:
In recent years, opposition MLAs in some states, such as Andhra Pradesh and Telangana, have broken away in small groups gradually to join the ruling party. In some of these cases, more than 2/3rd of the opposition has defected to the ruling party.
In these scenarios, the MLAs were subject to disqualification while defecting to the ruling party in smaller groups. However, it is not clear if they will still face disqualification if the Presiding Officer makes a decision after more than 2/3rd of the opposition has defected to the ruling party. The Telangana Speaker in March 2016 allowed the merger of the TDP Legislature Party in Telangana with the ruling TRS, citing that in total, 80% of the TDP MLAs (12 out of 15) had joined the TRS at the time of taking the decision.
In one of cases (Andhra Pradesh), the fact that the expulsion decision needs to be taken by the Presiding Officer of the assembly has also been exploited when the defections happened in the direction of the majority party... with the Presiding Officer delaying the decision for many months.
Although you didn't ask about this, there are a few other countries with somewhat similar anti-defection laws. Quite a few countries (about 40) have some penalties for legislators switching party, but only a few prohibit voting against the party line:
There are only 6 states (Guyana,
India, Pakistan, Bangladesh, Zimbabwe and Sierra Leone) where the constitution penalizes both defection
and voting against the party line.