No dictionaries, as far as I know, give anything other than ˌmæləˈɡæsi (or their idiosyncratic transcriptions of the same pronunciation, as in the new edition of the OED, with Upton’s a for æ).
Etymologically, the alternation between the d of Madagascar and the l of Malagasy is due to an alternation in the Malagasy language itself. The OED says
There is a division in Malagasy between dialects with /d/ and dialects with /l/, which accounts for the coexistence of forms in Mal- and forms in Mad-.
Wikipedia adds that Malagasy l becomes d “in reduplication, compounding, possessive and verbal constructions, and after nasals”. Malagasy belongs to the Bornean branch of the Malayo-Polynesian language family.
The other English adjective/ethnonym from Madagascar, namely Madagascan ˌmædəˈɡæskən, is interesting in that it is morphologically irregular. It “ought” to be Madagascarian, like Gibraltarian from Gibraltar. For non-rhotic speakers the irregularity is only in the spelling: as far as pronunciation goes, ˌmædəˈɡæskə — ˌmædəˈɡæskən is just like ˈæfrɪkə — ˈæfrɪkən.
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I feel quite chuffed that my lexical sets PALM and LOT have made it to lolPhonology.
As you can see, internal evidence (wif) suggests that this lolcat is American.