But not for the reason you suggest.
Article V says:
The Congress, whenever two thirds of both houses shall deem it necessary, shall propose amendments to this Constitution, or, on the application of the legislatures of two thirds of the several states, shall call a convention for proposing amendments, which, in either case, shall be valid to all intents and purposes, as part of this Constitution, when ratified by the legislatures of three fourths of the several states, or by conventions in three fourths thereof, as the one or the other mode of ratification may be proposed by the Congress; provided that no amendment which may be made prior to the year one thousand eight hundred and eight shall in any manner affect the first and fourth clauses in the ninth section of the first article; and that no state, without its consent, shall be deprived of its equal suffrage in the Senate.
So the composition of the Senate or its abolition can be done with a Constitutional Amendment (which, among other things, could remove this clause) only requires ratification by "three fourths of the several states"; that is, 38.
As to your specific question ...
The existence of the Senate and the number of senators is prescribed by the Constitution as 2 for each state so it would require a Constitution Amendment to abolish or change the number in any event. However, if it was changed to 1 or 3 or 12,764 for each state this would not violate the clause. So it could be done without changing this clause.
However, if you are making such a wholesale change anyway ...
As a point of interesting contrast
The Constitution says this:
Until the Parliament otherwise provides there shall be six senators for each Original State. The Parliament may make laws increasing or diminishing the number of senators for each State,5 but so that equal representation of the several Original States shall be maintained and that no Original State shall have less than six senators.
The Parliament has otherwise provided (several times) and there are now 12 Senators for each of the 6 states. Further, in 1975 the Parliament provided that the Northern Territory and Australian Capital Territory would have Senate representation of 2 Senators each - a controversial piece of legislation that needed to (and did) survive 2 separate High Court challenges.
In 1998, Territorians (people from the Northern Territory) rejected by referendum an offer of statehood that would have given them 3 senators - not being an "original state" this was perfectly Constitutional. The "Top End" is odd: if it were a state it would be the 3rd biggest by area (1,419,630 km2: 2.5 times the size of Texas) but the smallest (7th) by population (244,761, or less than half of the 6th biggest) - each person up there gets 5,800km2 compared to the world average of 0.068.